Download Investigating the role of papain-like cysteine protease RD21 in plant

Investigating the role of papain-like cysteine protease
RD21 in plant-pathogen interactions
Inaugural–Dissertation
zur
Erlangung des Doktorgrades
der Mathematisch-Naturwissenschaftlichen Fakultät
der Universität zu Köln
vorgelegt von
Takayuki SHINDO
aus Japan
Köln, April 2009
Die vorliegende Arbeit wurde am Max-Planck-Institut für Züchtungsforschung in Köln erstellt.
Berichterstatter:
Prof. Dr. Paul Schulze-Lefert
Prof. Dr. Reinhard Krämer
Prüfungsvorsitzende: Prof. Dr. Ute Höcker
Tag der Disputation: 29. April 2009
Contents
CONTENTS
Publications ................................................................................................................................................. I
Table of abbreviations .............................................................................................................................. II
Abstract .................................................................................................................................................... IV
Zusammenfassung ..................................................................................................................................... V
INTRODUCTION ....................................................................................................................................... 1
1.1
Classification and structure of papain-like cysteine proteases ............................................ 1
1.2
PLCPs in plants .................................................................................................................... 1
SAG12 …….................................................................................................................. 1
AALP ……................................................................................................................... 2
XCPs …….................................................................................................................... 3
1.3
Plant PLCPs acting extracellular defence ............................................................................ 4
Papain ……................................................................................................................... 4
Mir1 ……...................................................................................................................... 4
PIP1 ……...................................................................................................................... 5
RD19 …….................................................................................................................... 5
CatB ……..................................................................................................................... 5
1.4
Power of Activity-based protein profiling ........................................................................... 6
1.5
RD21 .................................................................................................................................... 6
1.6
Involvement of PLCPs in autophagy ................................................................................... 8
1.7
Towards functional analysis of RD21 ................................................................................. 9
RESULTS ................................................................................................................................................... 10
2.1
Phenotyping Arabidopsis PLCP mutants ........................................................................... 10
2.1.1 PLCP mutant collection .................................................................................... 10
2.1.2 Pathogen assays on rd21A knock-out lines ....................................................... 10
2.1.3 RD21A over-expression .................................................................................... 12
2.1.4 RD21 triple knock-out line ............................................................................... 13
2.2
Do PLCPs play a role in defence in tomato? ..................................................................... 15
2.2.1 Transcript level of some PLCPs up-regulated by BTH treatment .................... 15
2.2.2 Some PLCPs are under diversifying selection .................................................. 15
2.3
Analysis of NbRd21 silencing ............................................................................................ 18
2.3.1 Virus-induced gene silencing of RD21 in N. benthamiana .............................. 18
2.3.2 TRV::NbRd21 triggers cell death ...................................................................... 19
2.2.3 What is the trigger of cell death in NbRd21 silencing? ..................................... 22
2.3.4 Silencing autophagy-related genes pheno-copies NbRd21 silencing ................ 24
Contents
DISCUSSION ............................................................................................................................................. 26
3.1
Diversifying defence-related PIP1 and RCR3 ................................................................... 26
3.2
PLCPs in abiotic and biotic stress responses ..................................................................... 27
3.3
RD21 redundancy .............................................................................................................. 27
3.4
RD21 and TRV cause cell death ........................................................................................ 28
3.5
What is the biochemical function of RD21? ...................................................................... 29
3.6
Autophagy and RD21 ........................................................................................................ 30
3.7
Perspectives ........................................................................................................ 32
MATERIALS AND METHODS .............................................................................................................. 33
4.1
Chemicals and antibiotics .................................................................................................. 33
Enzymes ..................................................................................................................... 33
Vectors ....................................................................................................................... 33
Kits and primers ......................................................................................................... 33
Pathogens ................................................................................................................... 34
Bacterial strains .......................................................................................................... 34
Plant material ............................................................................................................. 34
4.2
Methods ............................................................................................................................. 34
Plant growth conditions ............................................................................................. 34
Plant transformation ................................................................................................... 35
Selection of transformants ......................................................................................... 35
Genomic DNA preparation ........................................................................................ 35
Crosses ....................................................................................................................... 36
Pathogen assays .......................................................................................................... 36
RNA isolation, cDNA synthesis and analysis and (quantitative) RT-PCR ............... 36
Cloning for VIGS ....................................................................................................... 37
Agrobacterium infiltration of virus-induced gene silencing construct ...................... 38
Co-infiltration of GFP and TRV vectors .................................................................... 38
Trypan blue staining ................................................................................................... 38
Generation of “hairpin” constructs ............................................................................ 38
Infiltration of virons ................................................................................................... 39
Western blot and Activity-based protein profiling .................................................... 39
Primers list .…………………………………………................................................ 40
APPENDIX ................................................................................................................................................. 44
REFERENCES .......................................................................................................................................... 47
ACKNOWLEDGMENTS ................................................................................................................... 57
ERKLÄRUNG .......................................................................................................................................... 58
LEBENSLAUF .......................................................................................................................................... 59
Publications
Publications
Shindo, T., and Van der Hoorn, R. A. L. (2008) Papain-like cysteine proteases: key
players at molecular battlefields employed by both plants and their invaders. Mol. Plant
Pathol. 9, 119-125. (some parts were used in introduction)
Shabab*, M., Shindo*, T., Gu, C., Kaschani, F., Pansuriya, T., Chintha, R., Harzen
A., Colby, T., Kamoun, S., and Van der Hoorn, R. A. L. (2008) Fungal effector
protein AVR2 targets diversifying defence-related Cys proteases of tomato. Plant Cell
20, 1169-1183.
Wang*, Z., Gu*, C., Colby, T., Shindo, T., Balamurugan, R., Waldmann, H.,
Kaiser, M., and Van der Hoorn, R. A. L. (2008) Beta-lactone probes identify a
papain-like peptide ligase in Arabidopsis thaliana. Nat. Chem. Biol. 4, 557-563.
I
Table of abbreviations
Table of abbreviations
::
fused to (in the context of gene fusion constructs)
%
percent
°C
degree Celsius
3’
three prime end of a DNA fragment
5’
five prime end of a DNA fragment
35S
double 35S promoter of CaMV
avr
avirulence
bp
base pair(s)
BTH
benzo(1,2,3)thiadiazole-7-carbothioic acid S-methyl ester
CaMV
cauliflower mosaic virus
cDNA
complementary DNA
cfu
colony forming unit
Col-0
Arabidopsis thaliana ecotype Columbia
d
dH O
day(s)
deionised water
2
DMSO dimethylsulfoxide
DNA
deoxyribonucleic acid
dNTP
deoxynucleosidetriphosphate
dpi
days post infiltration
DTT
dithiothreitol
E-64
(2S,3S)-3-(N-{(S)-1-[N-(4-guanidinobutyl)carbamoyl]3-methylbutyl}carbamoyl)
oxirane-2-carboxylic acid
EDTA
ethylenediaminetetraacetic acid
Emwa1 Hyaloperonospora parasitica isolate Emwa1
Fig.
Figure
g
gram
g
GFP
gravity constant (9.81 ms )
Green fluorescent protein
h
hour(s)
hp
hairpin-like structured
HR
hypersensitive response
HRP
horseradish peroxidase
kb
kilobase(s)
kDa
kiloDalton(s)
l
litre
-1
II
Table of abbreviations
Ler
Arabidopsis thaliana ecotype Landsberg erecta
m
milli
M
molar (mol/l)
µ
micro
min
minute(s)
mM
millimolar
N
amino-terminal
Noco2
600
Hyaloperonospora parasitica isolate Noco2
OD
optical density
PAD3
Phytoalexin Deficient 3
PCR
polymerase chain reaction
PAGE
polyacrylamide gel-electrophoresis
pH
PR
negative decimal logarithm of the H concentration
pathogenesis related
Pst
Pseudomonas syringae pv. tomato
pv.
Pathovar
PVX
Potato Virus X
R
resistance
RNA
ribonucleic acid
RNAi
double-stranded RNA interference
rpm
rounds per minute
+
RT-PCR reverse transcription-polymerase chain reaction
SA
salicylic acid
SGT1
Suppressor of G-Two allele of Skp1
SID2
Salicylic Acid Induction–Deficient 2
SDS
sodium dodecyl sulphate
sec
second(s)
TBS
Tris buffered saline
T-DNA transfer DNA
TMV
Tobacco mosaic virus
TRV
Tobacco Rattle Virus
VIGS
virus-induced gene silencing
Vir
virulence
Ws
Arabidopsis thaliana ecotype Wassilewskija
WT
wild-type
III
Abstract
Abstract
DCG-04 is a biotinylated derivative of cysteine protease inhibitor E-64, which
irreversibly reacts with papain-like cysteine proteases (PLCPs) when these proteases are
active. Using DCG-04, seven active proteases are labelled in Arabidopsis leaf extracts.
Of these, RD21 (responsive to desiccation-21) was found to have increased activity
during the infection with avirulent Pseudomonas syringe in Arabidopsis cell cultures.
Infection with a virulent strain caused post-translational suppression of RD21 activity.
These data suggest that RD21A plays a role in defence. We therefore challenged single,
double and triple knock-out lines of RD21-like proteases with several pathogens and
detected an altered susceptibility for Botrytis cinerea, but not the other pathogens tested.
Presumably because adapted pathogens might use inhibitors that make them insensitive
for RD21A.
As an alternative reverse genetic approach, we silenced the RD21 orthologs of
Nicotiana benthamiana using virus-induced gene silencing with Tobacco Rattle Virus
(TRV)-based silencing vectors. NbRd21 silencing resulted in retarded growth and
spreading cell death, most likely triggered by a combination of NbRd21 silencing and
TRV presence. Interestingly, silencing of autophagy-related genes, ATG3 and ATG6,
pheno-copied NbRD21 silencing. Furthermore, DCG-04 activity profiling assay showed
the suppression of NbRD21 activity and up-regulation of NbRd21 transcript in ATG3
(and ATG6) silenced plants, which implies a connection between RD21, cell death and
autophagy.
To identify other defence-related PLCPs, we applied benzothiadiazole (BTH)
to trigger the salicylic acid–regulated defence pathway in tomato. Of the seven PLCPs
tested, transcription of only PIP1 and RCR3 were induced. Sequencing of PLCP alleles
of tomato relatives revealed that same proteases, PIP1 and RCR3, are under diversifying
selection, resulting in variant residues around the substrate binding groove. Taken
together these data indicate that some PLCPs are involved in plant-pathogen
interactions.
IV
Zusammenfassung
Zusammenfassung
DCG04 ist ein biotinyliertes Derivat des Cysteinprotease Hemmstoffs E-64,
welcher irreversible mit papainähnlichen Cysteinproteasen (PLCPs) reagiert, wenn
diese in aktiver Form vorliegen. DCG-04 markiert sieben aktive Proteasen in
Arabidopsis Blattextrakten Eine dieser Proteasen, RD21 (Responsive to Desiccation-21),
weist eine erhöhte Aktivität während einer avirulent Pseudomonas syringae-Infektion in
Arabidopsis- Zellkulturen auf. Eine Infektion mit einem virulenten Pseudomonas
Stamm führte hingegen zu einer post- translationalen Unterdrückung der RD21
Aktivität, was vermuten lässt, dass RD21 eine Rolle in der Pathogenabwehr spielt. Um
diese Vermutung zu belegen, haben wir Einfach-, Doppel-und DreifachKnockoutmutanten der RD21- ähnlichen granulierten Proteasen verschiedenen
Pathogenen ausgesetzt. Dabei stellten wir fest, dass sich unter diesen Bedingungen nur
die Anfälligkeit gegenüber Botrytis cinerea verändert hat, vermutlich weil angepasste
Pathogene Hemmstoffe nutzen, um gegenüber RD21 weniger anfällig zu sein.
Um die Rolle von RD21 in N. benthamiana zu klären, haben wir die
genetisch-rückwärtsgerichtete Methode des Virus- induzierten Silencing (VIGS) mit auf
dem Tobacco Rattle Virus (TRV)-basierenden silencing Vektoren von
RD21-orthologen Genen durchgeführt. Dabei konnten wir beobachten, dass das
Unterdrücken von NbRD21 zu unterentwickeltem Wuchs und sich ausbreitendem
Zelltod führt, und vermuten, dass diese Reaktion höchstwahrscheinlich durch eine
Kombination von RD21A-Unterdrückung und dem Vorhandensein des
Silencing-Vektor TRV ausgelöst wurde. Interessanterweise hat das Unterdrücken der
Gene ATG3 und ATG6, die eine Rolle bei der Autophagie spielen, den gleichen
Einfluss auf die phenotypische Entwicklung von Nb wie das Silencing von RD21.
Zusätzlich konnte anhand von aktivitätsbezogenen Untersuchungen mit DCG04 einen
eine klare Verminderung des RD21-Signals in Pflanzen, in denen die Expression von
ATG3 und ATG6 unterdrückt ist, nachgewiesen werden, wobei das Transkriptionslevel
der Cysteinprotease erhöht ist. Diese Ergebnisse stützen die Annahme, dass ein
deutlicher Zusammenhang zwischen NbRd21, Zelltod und Autophagie besteht.
Um darüberhinaus weitere abwehrverwandten PLCPs zu identifizieren, nutzen
wir Benzothiadiazol (BTH), um den Salizylsäure-regulierten Abwehrmechanismus in
Tomate einzuleitet. Von sieben getesteten PLCPs wurde nur die Transkription von PIP1
und RCR3 induziert. Die Sequenzierung von PLCP-Allelen verwandter Species zeigte,
dass diese Proteasen, PIP1 und RCR3 unter Selektionsdruck stehen, was sich im
Auftreten unterschiedlicher Aminosäuren um die Substratbindestelle herum
V
Zusammenfassung
wiederspiegelt. Letztlich weisen diese Ergebnisse stark daraufhin, dass einige PLCPs
eine Rolle in Pflanzen-Pathogen Interaktionen besitzen
VI
Introduction
1
Introduction
In all organisms, non-functional proteins are degraded into amino acids by
proteases. Some proteases, however, are more selective and play key roles in signalling
cascades, regulating defence responses and during development (Van der Hoorn, 2008).
Proteases are grouped into four classes based on the active site nucleophile used;
cysteine, serine, methallo- or aspartic proteases.
1.1. Classification and structure of papain-like cysteine proteases
Proteases are grouped into families and clans in the MEROPS database based
on structural and evolutionary criteria (http://merops.sanger.ac.uk/, Rawlings et al.,
2008). To date, 70 families belonging to 12 different clans are cysteine proteases (Salas
et al., 2008). Family C1 (Cysteine protease 1) is subdivided into C1A and C1B. C1A
family members carry a signal peptide for the secretion and contain disulfide bridges.
Whereas, C1B family members are localised in the cytoplasm and do not contain
disulfide bridges (Rawlings et al., 2006). Plants only have C1A subfamily proteases
(Van der Hoorn, 2008). Papain-like cysteine proteases (PLCPs) belong to the family C1
of clan CA. PLCPs show the typical papain-like fold described by Drenth et al. (1968);
two domains, an α-helix-rich domain and a β-barrel-like domain, separating a
substrate-binding grove containing the active site (Figure 1.1.A). PLCPs are 23-30 kDa
in size and cleave peptide bonds of protein substrates using a catalytic cysteine residue
as a nucleophile. PLCPs are produced with an N-terminal auto-inhibitory domain
(called prodomain) which covers the substrate binding groove and needs to be
proteolytically removed for protease activation (Figure 1.1.B) (Taylor et al., 1995). The
actual auto-inhibitory motif in the prodomain is the conserved ERFNIN motif
(Grudkowska and Zagdanska, 2004). Some proteases carry a vacuolar targeting signal
(NPIR) in the prodomain and a predicted endoplasmic reticulum protein retention signal
(KDEL) at C-terminus (Grudkowska and Zagdanska, 2004).
1.2. PLCPs in plants
In Arabidopsis there are ~30 genes encoding PLCPs which can be subdivided
into 8 of subfamilies based on the phylogenetic similarities (Figure 1.2) (Beers et al.,
2004). To date only few have been studied in detail. These include SAG12, AALP and
XCP2 are described below.
SAG12 (Senescence-Associated Gene 12) is a well known senescence-marker
since its transcript level is up-regulated upon senescence and drought stress (Lohman et
al., 1994). Senescence specific regulation of SAG12 is tightly controlled by a highly
1
Introduction
Fig. 1.1
Characteristics of papain-like cysteine
proteases
A) Surface representation of the crystal structure of
papain, showing its wide substrate binding cleft with the
catalytic cysteine (yellow).
B) Domain structure of open reading frame of PLCPs of
family C1A. The signal peptide (sp) targets the protein
to the endomembrane system; the autoinhibitory
prodomain needs to be removed to activate the protease.
The protease domain contains three catalytic residues:
cysteine (C), histidine (H) and asparagine (N), and often
contains two disulphide bridges (SS).
conserved region of the SAG12 promoter (Noh and Amasino, 1999A, B). SAG12 is
localised in acidic senescence-associated vacuoles. During senescence, cells containing
these vacuoles shows the expression of SAG12 (Otegui et al., 2004). However, sag12
Arabidopsis mutants did not develop a phenotype under normal growth conditions and
during senescence (Otegui et al., 2004). This suggests that SAG12 is functionally
redundant with other proteases.
AALP (Arabidopsis Aleurain-Like Protease) is highly homologous to the
barley aleurain protease and is a well-known vacuolar marker protein (Ahmed et al.,
2000). In barley, this cysteine protease is synthesized in the endoplasmic reticulum and
transported through the Golgi to vacuole (Ahmed et al., 2000). Processing occurs before
the proprotease reaches the acidic compartment of cells and includes two steps; a
clipping step to remove prodomain and a trimming step to remove a small peptide
(Holwerda et al., 1990). The clipping step might require the activity of another cysteine
protease, called RD21 (see below for details) (Halls et al., 2005). Co-incubation of
proAALP with protease RD21 caused clipping and protease maturation (Halls et al.,
2005). A number of phenotypes have been reported for AALP. Suppression of transcript
levels of aleurain-like protease in Brassica oleracea, BoCP5, delays senescence (Eason
et al., 2005). Colletotrichum destructivum inoculation to N. benthamiana increases the
expression of AALP ortholog NbCYP1 and NbCYP1 silenced plants were more
susceptible (Hao et al., 2006). To date, no more Arabidopsis aalp mutant phenotype has
been reported.
2
Introduction
Fig. 1.2
Phylogenetic tree of papain-like cysteine proteases
Based on the phylogenetic similarities, plant PLCPs are subdivided into 8 subfamilies (colors in phylogenetic tree). The 31
Arabidopsis PLCPs are indicated with dots and protein domains are shown on the right. Sp, Signal peptide; Pro-, N-terminal
pro-domain; Protease, protease domain, with catalytic Cys (red); granulin, C-terminal granulin domain. The Gray region
between the protease and granulin is the proline-rich domain. Names with under line represents PLCP encoded from other plant
species. This phylogenetic tree is adapted and redrawn from Beers et al. (2004).
XCP1 and XCP2 (Xylem cysteine proteases) are two paralogs in Arabidopsis
which encode proteins sharing 70% identity (Beers et al., 2004). These genes are highly
expressed in flowers and stems, in particular in xylem but not in bark (Zhao et al., 2000).
XCP1 and XCP2 proteins are transported to the central vacuole of trachery elements
3
Introduction
during secondary cell wall thickening, suggesting XCPs are involved in autolysis of
trachery elements (Funk et al., 2002, Avci et al., 2008). Interestingly, recombinant
XCP1 becames only active at pH 5.5 and also the XCP homologue Tr-cp14 in white
clover (Trifolium repens) is activated at pH 5 (Zhao et al., 2000, Asp et al., 2004).
Ectopically expressed XCP1 in planta resulted in a reduction in plant size and early leaf
senescence phenotype (Funk et al., 2002). xcp1xcp2 double knock-out plants showed a
delay in clearing cellular remnants in vacuoles during autolysis (Avci et al., 2008). This
indicates that XCPs play a role as degrading enzymes in the xylem cells during
autolysis.
In short, PLCPs show a tight connection to plant senescence, probably due to
their role as degrading enzymes. But some PLCPs possess a specialised function in
plants.
1.3. Plant PLCPs acting extracellular defence
Plants use PLCPs to protect themselves against pests and pathogen attack.
Examples are papain from papaya and Mir1 from maize, both acting against insect
larvae. Tomato RCR3 and PIP1 are induced upon pathogen attack and inhibited by
pathogen-derived inhibitors. Arabidopsis RD19 is required for resistance against
bacterial pathogens. N. benthamiana CatB contributes to the defence response. These
PLCPs are described below.
Papain is a component of latex of papaya trees, which pours out of wounds,
presumably as a defence response against herbivores (reviewed by El Moussaoui et al.,
2001). The structure of papain was one of the earliest resolved protein structures
(Drenth et al., 1968). Papain is produced as a preproprotein, and mechanical wounding
of papaya fruit enhances papain accumulation and activation (Moutim et al., 1999;
Azarkan et al., 2006). However, the mechanism of its accumulation and how it is
activated is not clear, yet. A role of papain in insect defence has been described only
recently. Different lepidopteran caterpillars (Samia ricini, Mamestra brassicae and
Spodoptera litura) had reduced larval weight when fed with leaves containing papain
(Konno et al., 2004). This reduced growth was not the case when the latex was washed
out or when the leaves were treated with the cysteine protease inhibitor E-64 (Konno et
al., 2004). This indicates that papain contributes to defence against herbivores.
Mir1 (Maize imbred resistance 1) was identified because it was encoded by
an abundant transcript in callus of resistant but not susceptible maize when challenged
with armyworms (Spodoptera fugiperda) (Jiang et al., 1995; Pechan et al., 1999). Like
papain, Mir1 is translated as a preproprotein, suggesting that it is secreted or localized
4
Introduction
to vesicles. Mir1 protein accumulation occurs rapidly one hour after larval feeding,
continues for seven days and is most abundant at the feeding site (Pechan et al., 2000).
Tobacco budworm (Heliothis virescens) larvae fed with transgenic maize callus over
expressing the Mir1 gene were significantly smaller than those fed with callus from
control plants (Pechan et al., 2000; Chang et al., 2000). Feeding on resistant or Mir1
transgenic plants causes severe damage of the caterpillar peritorophic matrix, which is
the chitin structure covering the insect gut surface, protecting it from chemical and
physical damage (Pechan et al., 2002). It has been suggested that Mir1 can bind to
chitin, localizing the proteolytic activity to the insect gut (Pechan et al., 2002).
PIP1 (Phytophthora inhibited protease 1) and RCR3 (Required for
Cladosporium fulvum resistance 3) are two tomato PLCPs that accumulate in the
extracellularly in the apoplast (Krüger et al., 2002; Tian et al., 2007). Both PIP1 and
RCR3 map at the same genetic locus of tomato and are transcriptionally up-regulated
during pathogen challenge (Krüger et al., 2002; Tian et al., 2007). Both proteases are
inhibited by pathogen-derived inhibitors. PIP1 is inhibited by Epic2B, a cystatin-like
protease inhibitor secreted during infection by the oomycete Phytophthora infestans
(Tian et al., 2007). RCR3 is inhibited by Avr2, a secreted, cysteine-rich protein
produced by the leaf mould fungus Cladosporium fulvum (Luderer et al., 2002; Rooney
et al., 2005). The RCR3-Avr2 complex, and not RCR3 inhibition itself, triggers the
hypersensitive response (HR) mediated by tomato resistance gene Cf-2 (Rooney et al.,
2005). However, how Cf2 recognises the RCR3-Avr2 complex and the specificity of
inhibition by Avr2 and Epic2B are not yet fully understood.
RD19 (responsive to desiccation 19) is a drought stress-induced PLCP
(Koizumi et al., 1993). RD19 interacts with the effector protein PopP2 (Pseudomonas
outer protein P2) from soil-born bacterial pathogen Ralstonia solanacearum and is
required for resistance to R. solanacearum mediated by the RRS1-resistance gene
(Bernoux et al., 2008). A physical interaction between RRS1 and RD19 was not
detected. However, RD19 re-localised from vacuole compartment to the nucleus upon
PopP2 co-expression, suggesting that the nuclear complex is required for
RRS1-mediated resistance (Bernoux et al., 2008).
CatB (Cathepsin B) is another plant PLCP, named after the well-studied animal
Cathepsins which play a role in defence in animals (Zavasnik-Bergant and Turk, 2006).
Martinez et al. (2003) reported that the CatB gene in barley is ubiquitously expressed,
in particular in developing organs and under circadian control. CatB expression
increased upon cold shock, but was not altered by mechanical wounding (Martinez et al.,
2003). In potato, transcript levels of StCatB are induced at early stages of infection
5
Introduction
Phytophthora infestans on resistant plants (Avrova et al., 2004). Induced transcription
and CatB protease activity were also detected during the HR in N. benthamiana (Gilroy
et al., 2007). Importantly, CatB silencing suppresses the development of HR, suggesting
that CatB acts in defence signalling (Gilroy et al., 2007). Secretion of CatB into the
apoplast was observed and this secretion triggers maturation and activation of the
protease (Gilroy et al., 2007).
1.4. Power of Activity-based protein profiling
Knowing when a protease is active is crucial since proteases occur as inactive
precursors and are regulated by inhibitors. Activity-based protein profiling reveals the
activity of proteases through a covalent labelling of proteases with biotinylated
mechanism-based inhibitors, called probes (Greenbaum et al., 2000). This method is
widely applied in the medical field, but only starts to be used in plant science (Rooney
et al., 2005, Van der Hoorn, et al., 2004). A first example of activity-based protein
profiling in plants was by using DCG-04 (Van der Hoorn et al., 2004). DCG-04 is a
biotinylated derivative of E-64, an inhibitor of PLCPs, that irreversibly and covalently
reacts with the catalytic cysteine (Greenbaum et al., 2000). Using DCG-04 as a probe,
six PLCPs were detected in Arabidopsis leaf extracts (Van der Hoorn, et al., 2004).
These include three previously studied proteases (RD21, AALP and XCP2) and three
newly identified proteases, CatB1 (Cathepsin B-like protease 1), ALP2 (aleurain-like
protease 2) and THI1 (TPE4-like protease) (Yamada et al., 2001, Ahmed et al., 2000,
Zhao et al., 2000).
1.5. RD21A
RD21 (At1g47128) is a PLCP which was initially found to be up-regulated in
drought-stressed Arabidopsis and hence named responsive to desiccation-21
(Yamaguchi-Shinozaki et al., 1992). Although transcript levels of RD21 do not change
upon treatment with heat, cold nor abscisic acid, RD21 expression level increases upon
water deficiency (drought stress) and high salt conditions (Koizumi et al., 1993). RD21
contains an N-terminal signal peptide, a 20 kDa auto-inhibitory prodomain, a 33 kDa
protease domain, a 2 kDa proline-rich domain and a 10 kDa granulin-like domain
(Yamada et al., 2001). Protease maturation occurs in steps, starting from 1) signal
peptide release resulting in proRD21; 2) prodomain cleavage to form immature RD21
(iRD21); 3) granulin domain removal leading to mature RD21 (mRD21) (Figure 1.3).
Studies with recombinant RD21, produced in insect cells, revealed that the prodomain
cleavage is only triggered in the presence of plant extracts, indicating that the
6
Introduction
Fig. 1.3
RD21 maturation steps
RD21 maturation steps are shown. Preproprotein, precursor of
RD21; proRD21, proprotein precursor of RD21; iRD21,
intermediate RD21; mRD21, mature RD21; Sp, Signal peptide;
Pro-, N-terminal pro-domain; Protease, protease domain; P,
proline-rich domain; granulin, C-terminal granulin domain.
conversion of the proform into iRD21 is not autocatalytic (Yamada et al., 2001). What
triggers granulin domain removal is not understood, but both iRD21 and mRD21 are
active as protease (Yamada et al., 2001, Van der Hoorn et al., 2004). Localisation
studies indicate that iRD21 is transported from the Endoplasmic Reticulum (ER) with
ER bodies, small cellular organelles released from ER, in vacuoles, where conversion
into mRD21 occurs (Yamada et al., 2001, Hayashi et al., 2001, Carter et al., 2004,
Kikuchi et al., 2008).
RD21-like proteases that carry a C-terminal granulin domain are found in
many different plant species including tomato, maize, potato, rice, sweet potato, popla
and radish (Schaffer and Fischer, 1990, Linthorst et al., 1993, Tabaeizadeh et al., 1995,
Drake et al., 1996, Yamada et al., 2001B, Avrova et al., 1999, Chen et al., 2006,
Garcia-Lorenzo et al., 2006, Kikuchi et al., 2008). For example, in tomato, C14 (also
called as SENU2 or TDI-65) has been independently reported several times and C14
transcript levels are induced by cold, drought and during leaf senescence (Schaffer and
Fischer, 1990, Drake et al., 1996, Tabaeizadeh et al., 1995, Harrak et al., 2001). During
drought stress C14 is localized and accumulates upon in nuclei, chloroplasts and the
cytoplasm (Tabaeizadeh et al., 1995). The RD21-homologue of potato, CYP, is
transcriptionally induced in early stages of Phytophthora infestans infection (Avrova et
al., 1999). A maize RD21 homologue has been reported and remains to be
characterised (Yamada et al., 2001B).
A unique feature of RD21 is its C-terminal granulin domain containing 14
cysteines. The granulins have a size of approximately 6 kDa in animals and 10 kDa in
plants. Animal granulin proteins are encoded as tandem progranulins consisting of ~7
granulin domains, which can be released by processing (Bateman and Bennett, 1998).
Plant granulins contain two extra cysteine residues which probably form an extra
disulfide bridge within a putative extra β-hairpin (Tolkatchev et al., 2001, Yamada et
al., 2001). Plants encode genes only a single granulin domain in a C-terminal fusion
with PLCPs. Mammalian granulins are a family of growth factors that are expressed
and activated upon wounding (Bateman and Bennett, 1998, Guerra et al., 2007). A role
7
Introduction
of granulins in plants is yet poorly understood.
1.6. Involvement of PLCPs in autophagy
Autophagy, meaning “eat oneself” in Greek, is an intracellular recycling
system in eukaryotes, that recycles nutrients and degrade damaged or toxic
components in the cell (Seay et al., 2006). Autophagy is well characterised in yeast and
orthologs of yeast autophagy genes seem to be involved in autophagy in plants as well
(Bassham, 2007, Ketelaar et al., 2004). In plants there are two major autophagic
pathways, separated based on the capacity of cytoplasmic material taken up for
destruction; microautophagy and macroautophagy. Macroautophagy engulfs regions of
the cytoplasm into double-membrane autophagosomes which subsequently degrade the
inner contents (Bassham et al., 2006). While the digestion is taking place,
autophagosomes fuse with the vacuole and release the autophagic body (inner
compartment of autophagosome) into the lumen of the vacuole. In contrast,
microautophagy is formed from the vacuole membrane where small vesicles
containing cytoplasmis materials are released into the vacuolar lumen for degradation
(Bassham et al., 2006). Autophagosomes can also fuse with small lysosomes or
endosomes to form the autolysosome (Bassham, 2007). The contents of the
autolysosome is degraded before it fuses with the vacuole.
Several autophagy (ATG) genes are required for autophagy and these can be
grouped into five classes according to their functions; protein kinases, which are
involved in the initiation or regulation of autophagosome; the phosphatidylinositol
3-kinase complex; two ubiquitin-like conjugation systems and formation of ATG9
complex (Table. 1.1) (Bassham, 2007, Seay et al., 2006). Knock-out of ATG genes in
plants often display accelerated leaf senescence and defects in nutrient remobilization
during sugar and nitrogen starvation (Bassham, 2007). Autophagy in plants is also
involved in degradation of oxidised proteins and disposal of protein aggregates (Xiong
et al., 2007, Bassham, 2007). Moreover, like in animals, autophagy contributes to
innate immune responses since silencing of the ATG6/Beclin1 homologue in N.
benthamiana causes uncontrolled programmed cell death (PCD) upon infection with
avirulent tobacco mosaic virus (TMV) (Liu et al., 2005).
ATG8 is a ubiquitin-like proteins essential for autophagy (Ketelaar et al.,
2004). ATG8 modification requires two proteins, ATG3 and ATG4. ATG4 is cysteine
protease (Clan CA, family C54) that exposes the C-terminal Gly of ATG8 (Thompson
and Vierstra, 2005, Yoshimoto et al., 2004). ATG3 is an E2-like ligase that ligate
ubiquitin-like ATG8 after the C-terminal modification (Thompson and Vierstra, 2005,
8
Introduction
Table 1.1 Proteins involved in autophagy (Adapted from Bassham, 2007)
Function groups
Proteins
Regulation
TOR, ATG1, 13, 11, 19
Initiation of autophagy
PI-3 kinase complex
ATG6, VPS15, VPS34
Autophagosome formation
ATG5, 7, 10, 12, 16
Conjugation of ATG12 and ATG5
ATG3, 4, 7, 8
Conjugation of ATG8 to phosphatidylethanolamine
ATG9, 2, 18
Membrane recruitment to autophagosome
VTI12
Fusion of autophagosomes with the vacuole
Ubiquitin-like conjugation
ATG9 complex & localization
SNARE
Putative function
Tanida et al., 2006). Interestingly, plant cells incubated with E-64 or concanamycin A
result in the accumulation of autolysosomes in the cytoplasm during sugar starvation
(Bassham, 2007, Moriyasu et al., 2003, Inoue et al., 2006). Furthermore, E-64
inhibition of ATG8 modification, without inhibiting ATG4, has been reported (Alvarez
et al., 2008). Although, E-64 is a specific inhibitor of PLCPs, a contribution of PLCPs
to autophagy has not been reported so far.
1.7. Towards functional analysis of RD21
Previously, challenge of Arabidopsis cell suspension cultures with Pst
revealed that Pst infection leads to differential protease activities of RD21 (Renier van
der Hoorn unpublished data, done in John Iness Centre Norwich, UK). At 24 hours
post inoculation (hpi), RD21 activity was induced during infection with avirulent Pst
DC3000 AvrRpm1 and suppressed during infection with virulent Pst DC3000 (Van der
Hoorn, unpublished). Strikingly, RD21 protein levels remain similar. This
post-translational suppression of RD21 activity indicates that RD21 has a role in
plant-microbe interactions and that there is an RD21 inhibitor secreted by Pst. Indeed,
later during the cause of this PhD study, it was found that Pst secrets an
RD21-inhibiting protein (RIP1) (Kaschani and Van der Hoorn, unpublished). Also
Phytophthora infestans secrete inhibitors called EPIC protein preferentially target C14
(Shabab and Van der Hoorn, unpublished). These data prompted us to test if RD21A is
involved in defence.
9
Results
2
Results
2.1
Phenotyping Arabidopsis PLCP mutants
2.1.1
PLCP mutant collection
The Arabidopsis genome encodes for ~30 PLCPs which belong to eight
subfamily according to the phylogenetic analysis of plant PLCPs (Figure 1.2, Beers et
al. 2004). Hereafter, the above described RD21 is called as RD21A.
To study the role of PLCPs in plants, a collection of mutants was generated
from publicly available SALK or GABI collections. T-DNA insertions were confirmed
using gene-specific primers and homozygous mutant plants were selected and analysed
in subsequent generations. The mutants are listed in Table 2.1A. Double mutants of
homologous gene pairs, including rd21A x rd21B, rd21B x rd21D, rd21A x rd21D,
rd21A x rd21B x rd21D, aalp x alp2, xcp2 x xcp1 and catB1 x catB2, were generated
(Table2.1B). When activity-based DCG-04 profiling was applied to leaf extracts of this
mutant collection, signals were absent at 30 kDa and 25 kDa in rd21A and aalp
mutants, respectively (Figure 2.1.1). This is consistent with the identified proteases
described previously (Van der Hoorn et al. 2004), confirming that signals detected at
30 kDa and 25 kDa in DCG-04 profiles are predominantly caused by these two
proteases. None of the stable homozygous mutants displayed an obvious phenotype
when grown under normal greenhouse conditions.
Col-0 rd21-1 rd21-2 aalp
Figure 2.1.1.
Activity-based DCG-04 profiling of rd21 and aalp mutants.
40 -iRD21
DCG-04 protease activity profiles of leaf extract of rd21-1, rd21-2 and aalp
mutants. Molecular weight (in kDa) are indicated on the left of the image.
33 -
-mRD21
Biotinylated proteins were detected with streptavidin-HRP.
-AALP
24 -
2.1.2
Pathogen assays on rd21A knock-out lines
To test if RD21A plays a role in plant-microbe interactions, two independent
rd21A mutant lines (rd21A-1 and rd21A-2) were subjected to pathogen assays. Mutant
lines were challenged with Pst DC3000 and the bacterial growth was monitored up to 3
days post inoculation (dpi) by colony counting. rd21A lines did not show an increased
susceptibility when compared to wild type (Figure 2.1.2A). Similarly, infection with
avirulent strains expressing AvrRpm1 (Figure 2.1.2B), AvrRpt2 or AvrRps4 (data not
shown) did not display altered infection phenotypes. This indicates that growth of both
virulent and avirulent Pst is not affected in rd21A mutants.
10
Results
Table 2.1A
Gene
RD21A
Arabidopsis PLCP knock-out collection
Atg code
At1g47128
Source
Mutant
Transgenics
Atg codes
Gene
SALK_90550
rd21A-1
rd21AB
At1g47128
RD21A
SALK_90550
SALK_65256
rd21A-2
At5g43060
RD21B
SAIL_781H05
GABI_401H08
rd21A-4
At1g47128
RD21A
SALK_90550
GABI_792G08
rd21A-3
At5g43060
RD21B
SAIL_781H05
At1g09850
RD21D
SALK_138483
At4g35350
XCP1
SALK_84789
At1g20850
XCP2
SALK_10938
At5g60360
AALP
SALK_75550
At3g45310
ALP2
SALK_88620
At4g01610
CatB1
SALK_19630
At1g02305
CatB3
SALK_89030
At1g47128
RD21A
SALK_90550
At5g60360
AALP
SALK_75550
RD21B
At5g43060
SAIL_781H05
rd21B-1
RD21D
At1g09850
SALK_138483
rd21D-1
XCP1
At4g35350
SALK_84789
xcp1-1
XCP2
At1g20850
SALK_10938
xcp2-1
SALK_57921
xcp2-2
SAG12
At5g45890
SALK_124030
sag12.1
RD19A
At4g39090
SALK_31088
rd19A-1
AALP
At5g60360
SALK_75550
aalp-1
AALP2
At3g45310
SALK_88620
aalp2-1
CatB1
At4g01610
SALK_19630
catB1-1
CatB2
At1g02300
SALK_63455
catB2-1
SALK_110946
catB2-2
SALK_151526
catB2-3
SALK_89030
catB3-1
CatB3
At1g02305
Table 2.1B Double and triple PLCP mutants
rd21ABD
xcp1xcp2
aalp1alp2
catB1catB3
rd21Aaalp
Source
To test the susceptibility to other biotrophic pathogens, rd21A mutant lines
were challenged with Hyaloperonospora parasitica. rd21A-1 and rd21A-2 lines did not
show a significant increase in the number of spores at 7dpi upon inoculation with H.
parasitica isolate Noco2 (Figure 2.1.2C). Moreover, infection of rd21A lines with H.
parasitica isolate Emwa1 did not change the number of spores compared to wild type
plants at 7dpi (Figure 2.1.2D). rd21A mutant lines were also challenged with two
necrotrophic pathogens, Alternaria brassicicola and Botrytis cinerea, as well as the
semi-biotrophic pathogen Colletotricum higginsianum. Spread of the pathogen upon
droplet inoculation was scored at 5dpi. In case of C. higginsianum and A. brassicicola,
rd21A mutants did not show an altered susceptibility (Figure 2.1.2E,F). In contrast,
rd21A mutants were significantly more susceptible to B. cinerea inoculation, with 15 to
25% increased infection rates (Figure 2.1.2G). This shows that rd21A mutants are more
susceptible to the necrotrophic pathogen B. cinerea, but not to other pathogens tested.
11
Results
A
B
Pst DC3000 (-)
1.E+05
10
1.E+08
10
8
Col-0
rd21A-1
Col-0
rd21A-1
rd21A-2
sid2
rd21A-2
sid2
600000
1.E+05
105
104
Spores/1g of FW
1.E+06 6
10
H. parasi
parasitica
isolat eNoCo2
H.
ti ca isolate
Noc o2
500000
1.E+04
Growth log (cfu/cm)
Growth log (cfu/cm)
1.E+07
107
C
Pst DC3000 (AvrRpm1 )
5
1.E+03
103
400000
300000
200000
1.E+02
1.E+04
10
2
100000
104
1.E+01
1.E+03
0
(Days)
D
3
Col-0
E
100
100
C. higginsianum
H. parasitica isolat e EmWa
H. parasi ti ca isolat e Emwa
80
Infection (%)
200000
150000
100000
0
60
40
rd21A-1
rd21A-2
WS
eds1
A. brassicicola
60
40
20
0
Col-0
rd21A-2
80
20
50000
rd21A-1
F
Infection (%)
250000
Spores/1g of F W
0
(Days)
0
3
0
Col-0
rd21A-1
rd21A-2
pad3
Col-0
rd21A-1
rd21A-2
pad3
G
100
B. cinerea
Figture. 2.1.2 Phenotype of rd21 mutant lines upon infection with various
Infection (%)
80
pathogens.
60
All mutants are in Col-0 background. (A-B) rd21 mutants were challenged with
40
Pst DC3000 (-) (left) and Pst DC3000 AvrRpm1 (right). Number of
20
colony-forming units (cfu) were counted at 0 and 3dpi. The sid2 mutant was used
as a positive susceptible control and Col-0 as a negative control. Error bars
0
Col-0
rd21A-1
rd21A-2
pad3
represent standard deviation of 5 samples. (C-D) Hyaloperonospora parasitica,
Noco2 and Emwa, assays on rd21 knock-out lines. Spore counts were performed at 7dpi. Error bars represent the standard deviation of
3 samples. (E) Colletotricum higginsianum assay on rd21 knock-out lines. Plants were inoculated with droplets containing C.
higginsianum spores. Outgrowth was monitored at 5dpi. pad3 mutant was used as a positive control and Col-0 as a negative control.
Error bars represent standard deviation of 30 samples. (F) Alternaria brassicicola assay on rd21 knockout lines. Plants were inoculated
with droplets containing A. brassicicola spores. Outgrowth was monitored at 5dpi. Error bars represent the standard deviation of 30
samples. (G) Botrytis cinerea assays on rd21 knockout lines. Plants were inoculated with droplets containing B. cinerea spores. Spore
counts were performed at 7dpi. pad3 mutant was used as a positive control. Error bars represent the standard deviation of 10 samples.
2.1.4
RD21A over-expression
RD21A protein was over-expressed in planta to investigate if it causes a
phenotype. Full length RD21A was cloned into a plasmid behind the CaMV 35S
promoter and transformed into Agrobacterium (Van der Hoorn, unpublished). Transient
over-expression of 35S::RD21A by Agrobacterium infiltration into N. benthamiana
12
Results
resulted in high RD21A protein and activity levels, demonstrating that the construct is
functional (data not shown). However, no phenotype was observed upon infiltration
despite the fact that an active protease is over-expressed. The same construct was
stabely transformed into the ecotype Arabidopsis (Col) generating RD21A
over-expressing plants. Lines were selected that showed enhanced RD21A protein and
activity levels (data not shown). These lines did not display a phenotype under
standard greenhouse conditions. Pathogen assays with Pst (DC3000), H. parasitica
(Noco2), C. higginsianum, A. brassicicola or B. cinerea did not show any phenotype
when compared to wild-type Arabidopsis (data not shown).
2.1.5
RD21 triple knock-out line
There are four genes encoding granulin containing proteases in Arabidopsis,
named RD21A, RD21B (At5g43060), RD21C (At3g19390) and RD21D (At1g09850)
(Figure 1.2). Microarray data indicate that these proteases overlap in their expression
patterns in leaves and that only RD21C is distinctively expressed in roots (Appendix.
1) (Zimmermann et al., 2004, Genevestigator: https://www.genevestigator.ethz.ch). It
was hypothesised that the lack of phenotype during Pseudomonas infection was due to
redundancy with other granulated proteases. We, therefore, aimed at generating a
quadruple knock-out line lacking all granulated proteases to investigate the role of
these enzymes. Knock-out lines rd21B and rd21D were obtained from SAIL and
SALK line collections, respectively, and were confirmed by genomic PCR. T-DNA
insertion lines in RD21C were not available. We screened the Koncz T-DNA insertion
collection (Rios et al., 2002). Two candidates were found in the screening but the
T-DNA insertions in both cases were detected more than 50 bp after the end of open
reading frame (data not shown).
All possible double knock-out lines and the triple knock-out lines, rd21ABD,
were generated by crossing (Table. 2.1B). There was no phenotype observed under
normal greenhouse conditions. To test if the absence of three granulated proteases
alters pathogen susceptibility, the triple rd21ABD knock-out line was challenged with
various pathogens. The rd21ABD triple knock-out line was not more susceptible to Pst
(DC3000), H. parasitica (both Noco2 and Emwa1), C. higginsianum and A.
brassicicola compared to wild-type Arabidopsis (Figure 2.1.3A-E). In the case of B.
cinerea inoculation, however, there was approximately 30% increase of fungal
infection when compared to wild-type (Figure 2.1.3F-G). This indicates that rd21ABD
show the increased susceptible phenotype to B. cinerea, but not other pathogens tested.
13
Results
A
B
C. h iggi nsi an um
P st DC30 00.
Col- 0
rd21 AB D
Co l- 0
si d 2
C
r d2 1A BD
Ler
D
H. p ar asi tica Emwa
H. par asi tica Noco 2
Col- 0
r d2 1A BD
Ws
Co l- 0
E
r d21A BD
Ws
F
A . br assi cicola
B . cin er ea
Co l- 0
r d2 1A BD
Col -0
pa d3
rd21ABD
pad3
G
100
B. cinerea
Figure. 2.1.3 Phenotype of rd21ABD triple knock-out.
80
Infection (%)
(A) Phenotype upon infection with Pst DC3000. Plants were spray-inoculated
60
with Pst DC3000 (OD600=0.001) and photographed at 4dpi. sid2 mutant was
40
used as a susceptible control. (B) Spray inoculation of C. higginsianum to
20
rd21ABD triple knock-out plants. Spore suspension was sprayed and pictures
were taken at 5dpi. Ler was used as susceptible control. (C-D) H. parasitica,
0
Col-0
rd21ABD
pad3
Noco2 (left) or Emwa1 (right), challenge to rd21ABD triple knock-out.
Spore suspension was sprayed and pictures were taken at 7dpi. In both cases, ecotype Ws was used as a control. (E) Droplet
inoculation of A. brassicicola to rd21ABD triple knock-out. Spore suspension was used for droplet inoculation. At 5dpi
inoculated leaves were detached and photographed. pad3 was used as a positive susceptible control. (F) Droplet inoculation
of B. cinerea on rd21ABD triple knock-out. A droplet of spore suspension was inoculated on a leaf. Pictures were taken at
5dpi. (G) Percentage of B. cinerea outgrowth in rd21ABD was determined. Error bars represent the standard deviation of
100 samples. pad3 was used as a susceptible control.
14
Results
2.2.
Do PLCPs play a role in defence in tomato?
The following section was a part of Shabab et al. 2008 is shown below. This
was accomplished together with R. A. L. Van der Hoorn.
2.2.1.
Transcript level of some PLCPs up-regulated by BTH treatment
BTH is an analogue of salicylic acid (SA) and triggers the salicylic acid
dependent defence pathway in plants (Achuo et al., 2004). To investigate if any of the
PLCPs are also regulated by SA, transcriptional changes of genes encoding PLCPs
were studied after BTH treatment. As shown in figure 2.2.1A, transcript levels of two
PR (Pathogenesis Related) genes, PR1 and PR4, significantly increased at 5 days after
BTH treatment. Accumulation of transcripts occurred also for genes encoding PIP1
and RCR3 (Figure2.2.1A). The other PLCPs tested (C14, Cyp3, Alp, CatB1 and CatB2)
were not induced by BTH treatment to high levels. Quantitative RT-PCR revealed that
there was an eight-fold induction of both Pip1 and RCR3 upon BTH treatment, while
there were only minor or no changes in the other genes tested (Figure 2.2.1B).
A
A
H O BTH
H 2O B TH
H2O BTH
H O BTH
H2O BTH
H O BTH
PR1
C14
Cyp3
PR4
Pip1
Alp
Actin
Rcr3
CatB1
Figure 2.2.1
Induction of transcript levels of
tomato PLCPs upon BTH treatment.
Tomato leaves were harvested at 5 days after
water or BTH treatment.
CatbB2
(A) RT-PCR was performed using gene-specific
B
B
primers. Actin was used as a control.
(B)
Quantitative
real-time
RT-PCR
was
performed using gene-specific primers. The
difference in threshold cycles (dCt) between the
protease transcript and ubiquitin transcripts was
calculated from three independent samples. Error
bars represent SD. A representative of five
independent biological experiments is shown.
2.2.2. Some PLCPs are under diversifying selection
Defence-related enzymes might be involved in antagonistic interactions with
pathogens-derived substrates or inhibitors (Misas-Villamil and Van der Hoorn, 2008).
15
Results
Figure 2.2.2 Sequence analyses of PLPCs from tomato relatives.
(A) Summary of amino acids encoded by variant codons in the protease domains of C14, PIP1, RCR3, CYP3, ALP, CatB1, and
CatB2 alleles sequenced from various wild tomato relatives (indicated top right). Amino acids encoded by the variant codons
are summarized by leaving out the amino acids of nonvariant codons from the protein alignment. Amino acids encoded by
codons different from the S. lycopersicum (lyc) allele are indicated with gray, blue, and red residues if they are identical,
similar, or nonsimilar, respectively, compared with the lyc sequence. Dashes indicate missing sequence information. RCR3 of
S. cheesmanniae is not shown since it contained a premature stop codon and could be amplified from genomic DNA and not
from cDNA.
16
Results
(B) Number of single nucleotide (nt) polymorphisms per protease. (C) Ratio of nonsimilar/similar amino acid (aa) substitutions
calculated from (A). PIP1 and RCR3 are under diversifying selection; the other proteases are under conservative selection.
(D) Position of variant residues in structural models of PIP1 and RCR3. Positions with nonsimilar variance and similar variance
are indicated in red and blue, respectively.
To investigate if tomato PLCPs are under evolutional selection to be diverse, we
sequenced the region encoding the protease domain of eight wild tomato relatives: S.
cheesmanniae, S. pimpinellifolium, S. chilense, S. pennellii, S. habrochates (hirsutum),
S. peruvianum, S. schiewlskii, and S. parviflorum. Sequences of theses alleles were
validated and found to be 98% identical to the reported tomato sequences. Amino acids
encoded by the polymorphic codons of all the protease domains are shown in Figure
2.2.A. The protease-coding part of each gene contains about 20 variant nucleotides,
except for RCR3, which has 41 variant nucleotides (Figure 2.2.2B). Some of the variant
nucleotides are shared among different species, indicating that part of the variation
predates speciation (Figure 2.2.2A). Most of the polymorphic nucleotides, however, are
allele-specific. The consequence of these variant residues at amino acid level is striking.
Variant codons hardly change the encoded amino acids in C14, CYP3, ALP, CatB1, and
CatB2 (Figure 2.2.2A, bottom, white and gray residues). By contrast, nearly all variant
codons of PIP1 and RCR3 cause nonsimilar amino acid substitutions (Figure 2.2.2A,
bottom, red residues). The ratio between nonsimilar and similar amino acids indicates
that C14, CYP3, ALP, CatB1, and CatB2 are under conservative selection, whereas
PIP1 and RCR3 are under diversifying selection (Figure 2.2.2C). Taken together, these
observations demonstrate that PIP1 and RCR3 are under diversifying selection,
possibly to adapt to diversifying substrates or inhibitors, whereas the other proteases
are under conservative selection.
17
Results
2.3
Analysis of NbRd21 silencing
2.3.1.
Virus-induced gene silencing of RD21 in N. benthamiana
When the protein sequence of the granulin domain of Arabidopsis RD21A was
blasted at TIGR using tBLASTn (http://plantta.tigr.org/), there were two highly
homologues cDNA sequences found in N. benthamiana, NbRd21-I (TC7740/
CN743238) and NbRd21-II (EST748747/CK286025). NbRd21-I encodes a full length
protease whereas NbRd21-II is incomplete at the 5’ end and only encodes part of the
protease domain followed by granulin domain. There is a 362 bp region 81%
homology in both NbRD21-I and NbRd21-II on nucleotide level (Figure 2.3.1A,
coloured in yellow). The amino acid sequence NbRd21-I is 42% identical and 58%
similar to C14 of tomato and 43% identical and 59% similar to RD21B in Arabidopsis.
Three regions of about 300 bp were selected from NbRd21-I (α, β and γ) and one from
NbRd21-II to generate TRV-based silencing constructs. NbAlp (TC7311) was taken as a
protease control for silencing. The NbAlp encodes a protease that is 78% identical to
Arabidopsis AALP.
TRV-based virus-induced silencing was initiated by infiltrating Agrobacterium
cultures carrying the binary TRV constructs into four week-old N. benthamiana plants.
TRV constructs containing fragments of GFP or NbAlp were used as controls for
silencing. Semi-quantitative RT-PCR on RNA isolated from systemic leaves at 21 dpi
confirmed selective silencing (Figure 2.3.1B.). Importantly all NbRd21 silencing
constructs suppress transcript levels of both NbRd21 genes (Figure 2.3.1B.). Thus, all
NbRd21-I silencing constructs co-silence NbRd21-II and vice-versa. Silencing of
NbRd21 was not observed in plants inoculated with TRV::Alp or TRV::GFP, but NbAlp
transcript levels are dramatically reduced in TRV::Alp plants (Figure 2.3.1B.).
Quantitative real-time RT-PCR showed that in TRV::NbRd21-I plants the transcript
levels of NbRd21-I and NbRd21-II are reduced by 80% and 65%, respectively (Figure
2.3.1C.). In contrast, in TRV::NbRd21-II plants, transcript levels of NbRd21-I and
NbRd21-II are reduced by 40 and 85%, respectively (Figure 2.3.1C.). This implies that,
although transcript levels of both genes are suppressed, the genes corresponding to the
silencing construct are more severely silenced. No difference in the silencing level was
observed between all three independent NbRd21-I silencing constructs.
To study the effect of silencing on protease activity levels, activity-based
profiling using DCG-04 was performed on protein extracts from systemic leaves of
silenced plants. Activity profiles of TRV::GFP plants show bands at 40, 33, 30 and 28
kDa (Figure 2.3.1D.). In Arabidopsis leaf extract, signals of 40 and 33 kDa are caused
18
Results
AA
α
NbRD21-I
(TC7740)
S Prodom
β
γ
P r o te a se
TRV::
BB
Alp
Rd21-II
Rd21-I
α
GFP
β
NbRd21-I
P Gran
81%
NbRd21-II
NbRD21-II
(EST748747)
Alp
Actin
C
NbRd21 transcript leve l on
N. benthamiana, 5wpi of TRV constructs
C
D
D
1.5
Relative Expression to GFP
NbRd21-I
NbRd21-II
TRV::
GFP
i-NbRD21 >
NbRd21-II NbRd21-I +E64
NP
< 43
1
m-NbRD21 >
< 33
0.5
Alp >
0
TRV::
NbRd21-I
Figure 2.3.1
NbRd21-II
< 26
GFP
NbRd21 silencing constructs co-silence both NbRd21-II and NbRd21-II
A) Fragments used for silencing constructs. Two cDNA sequences encoding RD21-like proteases of N. benthamiana are available
at the TIGR database. The sequence of NbRd21-II is incomplete (dashed lines). Lines above the bars indicate the regions used for
silencing constructs for virus-induced gene silencing (VIGS). The region coloured in yellow indicates 81% nucleotide identity. S,
Signal peptide; Prodom, N-terminal pro-domain; Protease, protease domain; P, proline-rich domain; Gran, C-terminal granulin
domain. B) Transcript levels in systemic leaves of N. benthamiana plants inoculated with various silencing constructs at 28 dpi.
Gene-specific primers were used for semi-quantitative RT-PCR. Actin was used as a control. C) Transcript levels in systemic
leaves of N. benthamiana plants inoculated with NbRd21 silencing constructs at 28 dpi. Gene-specific primers were used for
Realtime RT-PCR. Transcript levels were normalised to that of GFP silenced plants. D) DCG-04 activity profiling on extracts of
systemic leaves of silenced plants at 28 dpi. NP, no probe control; +E-64, excess of E-64 to compete for DCG-04 labelling.
by the immature (i) and mature (m) isoform of RD21A, respectively, whereas the 28
kDa signal represents AALP (Van der Hoorn et al., 2004). In both TRV::NbRd21-I and
TRV::NbRd21-II plants, both 40 and 33 kDa signals were reduced whereas the 28 kDa
signal is as intense compared to TRV::GFP plants (Figure 2.3.1D.) indicating that
NbRd21 silencing suppresses NbRD21 activity in systemic leaves.
2.3.2.
TRV::NbRd21 triggers cell death
Importantly, all TRV::NbRd21 plants showed retarded growth at 14 days after
infiltration (Figure 2.3.2A.). By 28 dpi there was a clear growth retardation of
19
Results
A
TRV::
TRV::
TRV::
TRV::
TRV::
Rd21-Iβ
Rd21-1γ
Rd21-II
Alp
GFP
2 weeks
A
BB
4 weeks
Fresh weight (g)
10
5
0
TRV::
Rd21-I
Rd21-II
Alp
GFP
Figure 2.3.2 Phenotype of N. benthamiana upon virus induced gene silencing of NbRd21
(A) 4-week old N. benthamiana plants were infiltrated with Agrobacterium carrying binary TRV constructs, and photographed at
2 and 4 weeks after infiltration. TRV::Alp (Aleurain-like protease) and TRV::GFP were used as controls. (B) Fresh weight of
plants at 5 weeks after inoculation with TRV constructs. Results shown represent the average weight of three plants. Error bars
represent SD. A representative of three biological replicates is shown.
TRV::NbRd21 plants in contrast to TRV::Alp or TRV::GFP plants, both in size and
weight (Figure 2.3.2B.). When the plants were more carefully investigated,
TRV::NbRd21 plants showed cell death on both the infiltrated leaf and the leaf above
the infiltrated leaf.
To monitor cell death development in more detail, TRV constructs were
infiltrated into mature leaves of N. benthamiana. No difference was observed between
TRV::GFP and TRV::NbRd21 infiltrated leaves during the first two days. At 3 dpi,
however, cell death started to appear in and around the TRV::NbRd21 infiltrated region
(Figure 2.3.3A.). This was followed by the formation of a ring-shaped cell death at 4 to
5 dpi surrounding the infiltrated zone (Figure 2.3.3A.). The cell death eventually
spread out through the leaf as well as inside the infiltrated zone by 9 dpi (Figure
2.3.3A.). In many cases, spreading of cell death reached the vein of the leaf in seven
days and migrates to the stem and upper leaves within 14 days.
In order to characterize how the cell death spreads, TRV::NbRd21-infiltrated
leaves were stained with trypan blue that stain dead cells blue. This assay revealed that
spots of cell death develop in the infiltrated region at 3 dpi (Figure 2.3.3B.). These
spots of cell death were larger on the edge of the infiltrated zone than inside the
infiltrated area (Figure 2.3.3B.). Formation of the ring-shaped cell death occurs around
the TRV::NbRd21 infiltrated area at 5 dpi which leads to the cell death spreads (Figure
2.3.3B.). No cell death was detected in TRV::GFP infiltrated leaves at any of the
20
Results
AA
2dpi
3dpi
4dpi
5dpi
9dpi
TRV::GFP
TRV::Rd21-I
TRV::Rd21-II
TRV::Alp
BB
3dpi
5dpi
TRV::G FP
TRV::Rd 21
TRV ::GFP
C
5dpi
TRV::Rd21
DD
TRV::Alp
TRV::RD21-I
TRV::RD21-II
TRV::GFP
Bright
field
O uOutside
tsi d e ( O
)
(O)
GFP
Ri ng
Ring
(R)( R)
InfiltratedInfi
(I) l tra ted (I)
4dpi
O
R
I
O
R
I
Rd21
TRV
Merge
Figure 2.3.3
Actin
Cell death develops around the infiltrated region of TRV::NbRd21
(A) Infiltration of TRV constructs into mature N. benthamiana leaves. Images were taken at different days post infiltration (dpi).
(B) Trypan blue staining of TRV infiltrated leaves. Infiltrated leaves (top) were stained by Trypan blue (bottom); dead cells are
stained blue. (C) Cell death develops around the infiltrated region. TRV constructs were co-infiltrated with a GFP construct.
Pictures were taken at 5dpi with a fluorescence microscope under bright field and under GFP filter. (D) Transcript level of in and
around the infiltrated area. As the schematic diagram (top) shows, leaves infiltrated with TRV::NbRD21 or TRV::GFP were
sampled in three different sections; Infiltrated (I), Ring around the infiltrated region (R) or Outside (O). RT-PCR was performed
to detect transcript levels of NbRd21, TRV and actin (control).
21
Results
analysed time points.
To specify the region where the cell death ring develops, TRV::NbRd21
constructs were co-infiltrated with Agrobacterium containing a 35S::GFP binary
construct. This method enables us to visualize the infiltrated zone by GFP fluorescence.
At 5 dpi the cell death ring was formed precisely along the edge of the fluorescent area
(Figure 2.3.3C.). This demonstrates that cell death occurs in the Agrobacterium-free
region, surrounding the infiltrated zone.
To detect transcript levels in and around the infiltrated area, three samples
were taken from Agrobacterium infiltrated leaves; the infiltrated region (I), the edge of
infiltrated zone (R, where cell death “ring” would occur at 5dpi) and further outside the
infiltrated area (O) (Figure 2.3.3D.). Sample collection took place at 3dpi before the
ring of cell death appears. The three portions of leaves were analysed by
semi-quantitative RT-PCR. TRV::NbRd21 infiltration suppresses NbRd21 transcript
levels already at 3dpi in the infiltrated region and, interestingly, in the ring as well
(Figure 2.3.3D.). In contrast, RNA levels of the TRV is high in all regions at 3dpi,
implying that TRV movement is a fast process that causes TRV RNA accumulation
outside the infiltrated area. Taken together these results indicate that cell death in the
ring is preceded by strong NbRd21 silencing
2.3.3.
What is the trigger of cell death in NbRd21 silencing?
Since the transient expression system used to introduce TRV::NbRd21
inevitably introduces also Agrobacterium, it was not clear if Agrobacterium contributes
to the cell death phenotype. To rule out the potential Agrobacterium involvement to
cell death, sap containing virions isolated from TRV::NbRd21 and TRV::GFP plants at
four weeks after inoculation (Figure 2.3.4. left). When sap containing TRV::NbRd21
virions were injected into leaves of new N. benthamiana plants, the inoculation
resulted in spreading cell death at 5 dpi (Figure 2.3.4. right). Sap containing TRV::GFP
virions or leaf extract from non-infected plants did not trigger cell death. Additionally,
no Agrobacterium was detected when sap was plated on kanamycin and rifampicin
containing plates, implying there was no Agrobacterium in the sap (data not shown).
This demonstrates that Agrobacterium is not required for TRV::NbRd21 induced cell
death.
In order to uncouple NbRd21 silencing from TRV, RNAi hairpin (hp)
constructs, hpNbRd21, were generated using the same fragments from NbRd21 used to
generate the TRV::NbRd21 constructs. RT-PCR at 5 dpi of hpNbRd21-infiltrated leaves
showed reduced NbRd21 transcript levels in the infiltrated region (data not shown).
22
Results
A
B
5dpi
Virus
TRV :G FP
Ctr
TRV::RD21 -1β
Ctr
Sap of TRV
AgroInfiltrated!
28dpi TRV
Leaf extract
New plant
infected plant
Figure 2.3.4
Cell death is induced by TRV::NbRd21 in the absence of Agrobacterium
(A) Infiltration of TRV virus to mature leaves. Virions, isolated from TRV-infected plants at 4 weeks after infiltration, were
infiltrated to non-silenced mature leaves (left half of leaves). (B) Images were taken (top) and leaves were stained by Trypan
blue (bottom). Control (Ctr) leaf extract was isolated from non-infected plants and infiltrated in the right half of the leaves
However, despite hpNbRd21 silencing, no cell death or other phenotypic changes were
observed (data not shown). This implies that TRV is needed as an inducer of cell death.
Therefore, hpNbRd21 was co-infiltrated with TRV::GFP to reconstitute the cell death
phenotype. However, co-infiltration of both TRV and hpNbRd21 did not result in
spreading cell death (Figure 2.3.5A).
To test if the cell death inducer can be replaced, several potential inducers
were tested in leaves with low NbRD21 levels. Matching resistant gene (R) and
avirulence gene (AVR) couples lead to gene-for-gene interactions, triggering
programmed cell death, HR (Gilroy et al., 2007). Combinations of Rx and CP, Cf4 and
Avr4 as well as N and P50 were used to trigger HR. TRV::SGT1 plants which cannot
develop HR were included in assay to confirm if developed cell death was really HR
(Peart et al., 2002, Azevedo et al., 2006). Although HR develops normally in these
plants, none of the HR inducers did promote spreading cell death in NbRd21 silenced
plants (Figure 2.3.5B). Other cell death inducers such as methanol infiltration,
mechanical damage, TMV (tobacco mosaic virus) and PVX (Potato virus X) did also
not trigger spreading cell death (data not shown).
23
Results
A
B
HpNbRD21-II
NbR d21 f ragment
Ins ert
HpNbRD21-II
NbR d21 fragment
35s
HpGFP
HpAlp
TRV :: A lp TRV::Rd 2 1 -I
TRV ::S G T1 T RV:: G FP
TRV::GFP
Figure 2.3.5. Uncoupling cell death inducers: TRV-independent transient silencing (even by adding TRV) nor HR
inducers do not trigger spreading cell death
(A) Co-infiltration of hairpin silencing constructs with TRV::GFP (full length). Inverted repeat constructs (hp; hairpin), were
used as local silencing inducer. Bright field and GFP fluorescence image were taken at 5dpi. (B) Infiltration of cell death
inducers into systemic leaves of plants infected with TRV constructs. Cell death inducers Rx+CP were infiltrated into systemic
leaves of plants. HR insensitive TRV::SGT1 was used as negative control for confirming the cell death is HR.
2.3.4.
Silencing autophagy-related genes pheno-copies NbRd21 silencing
Liu et al. (2005) showed that when autophagy related genes are silenced in N.
benthamiana, spread of cell death cannot be restricted. This phenotype could be similar
to the TRV::NbRd21 phenotype. Fragments of six autophagy-related genes (Atg7, Atg6,
Atg3, Atg5, PI3K and Atg8e) were selected for TRV-based virus-induced gene silencing.
TRV::Atg3 plants showed a retarded growth at 28 dpi and a cell death phenotype at 14
dpi, similar to TRV:: NbRd21 plants (Figure 2.3.6A). TRV::Atg6 plants also showed a
cell death phenotype, but weaker than TRV::Atg3 or TRV::NbRd21 plants (Figure
2.3.6B). TRV::Atg3 infiltration in mature leaves caused a ring-shaped cell death at 5
dpi, similar to TRV::NbRd21 (Figure 2.3.6C). Infiltration of TRV::Atg3 virions to
non-inoculated plants initiated cell death (Figure 2.3.6D). Thus, Atg3 silencing
pheno-copies NbRd21 silencing.
The phenotypic similarities suggested a molecular link between NbRd21 and
autophagy. To investigate that, we monitored NbRd21 transcript levels and NbRD21
activity in TRV::Atg3 plants. Transcript levels in systemic leaves of TRV::Atg3 and
TRV::Atg6 plants were up-regulated when compared to TRV::GFP plants (Figure
2.3.6E). Activity-based profiling with DCG-04 on systemic leaves of TRV::Atg3 and
TRV::Atg6 plants showed a reduced 40 kDa signal of iNbRD21 similar to that of
TRV::NbRd21 plants (Figure 2.3.6F). In contrast, the intensity of the Alp signal is
unaltered in TRV::Atg3, TRV::Atg6 and TRV::NbRd21 plants. This implies that
silencing of Atg3 or Atg6 leads to a decrease of NbRd21 activity, while the NbRd21
transcript level is up-regulated, indicating that Atg3 or Atg6 silencing hampers
NbRD21 function.
24
Results
AA
B
B
TRV::
TRV::
TRV::
TRV::
TRV::
TRV::
TRV::
GFP
Atg7
A tg6
Atg3
Atg5
Pi3K
Atg8e
TRV::RD21-I
D
TRV::RD21-II
D
TRV::Atg3
TRV::GFP
Cnt
TRV::Atg3
Cnt
TRV::Atg3
E
E
TRV::
NbRd21
Atg6
Atg3
GFP
NbRd21
C
Actin
C
2dpi
3dpi
4dpi
5dpi
9dpi
F
F
TRV::GFP
TRV::
G FP
NbRd 21
II
I
Atg 6 Atg 3 P I3K Atg 7 E- 64 NPC
< 43
i-NbRD21 >
TRV::Rd21-I
m-NbRD21 >
Alp >
< 33
< 26
TRV::Atg3
Co o ma ssi e
Figure 2.3.7 Analysis of autophagy-related gene silenced plants.
(A) Silencing of some of autophagy-related genes. Fragment of Atg7, Atg6, Atg3, Atg5, PI3K and Atg8e were used for
TRV-based silencing constructs. Images were taken at 28dpi. (B) Cell death phenotype of TRV::Atg3 plants compared to
TRV::NbRd21 and TRV::GFP plants at 14dpi. (C) Infiltration of TRV::Atg3 into mature leaf. Infiltrated leaves were monitored
up to 9dpi. (D) TRV::Atg3 virons inoculated into new leaf (left). Dead cells were stained with Trypan blue at 5 dpi (right).
(E) Transcript analysis of systemic leaves of silenced plants. RNA of TRV::NbRd21, TRV::Atg6, TRV::Atg3 and TRV::GFP
plants were isolated and subjected to semi-quantitative RT-PCR using gene specific primers of NbRD21 (top) and actin (bottom).
(F) DCG-04 protease activity profiles of systemic leaves of silenced plants. Activity-based protein profiling with DCG-04 was
performed on systemic leaves, at 28 dpi with various constructs (Top). Corresponding coomassie stained gel is shown as control
(Bottom). NP, no probe control; +E-64, addition of excess E-64 to compete DCG-04 labelling. Molecular weight (in kDa) are
indicated to the right of the image.
25
Discussion
3
Discussion
Here we have shown that Arabidopsis RD21A contributes to resistance to B.
cinerea. Moreover, it was demonstrated that virus-induced gene silencing of NbRd21
triggers cell death, probably initiated by Tobacco Rattle Virus. This
TRV::NbRd21-induced cell death is pheno-copied by silencing autophagy related genes
and NbRD21 activity is hampered in Atg3 and Atg6 silenced plants. Furthermore,
transcript levels of tomato apoplastic-space secreted PLCPs, RCR3 and PIP1, are
induced upon BTH treatment and the proteases are under high evolutional selection
pressure to diversify.
3.1
Diversifying defence-related PIP1 and RCR3
Although the idea that PLCPs act in biotic stress responses is relatively new
(Van der Hoorn and Jones, 2004), transcriptional changes of PLCPs upon abiotic
stresses, including drought, cold, ABA, have been reported since decades (Grudkowska
and Zagdanska, 2004, Harrak et al., 2001, Lohman, et al., 1994). Connections of
PLCPs to drought stress and senescence have been well described. Good examples are
Sag12 and AALP homologues (Lohman, et al., 1994, Eason et al., 2005). Both
proteases are in vacuole, presumably degrading proteins during senescence. Some
PLCPs react to both drought and senescence, but some respond to these conditions
independently (Beyene et al., 2006).
Our data indicate that PIP1 and RCR3 belong to the class of PR proteins that
accumulate during the immune response via SA signalling pathway (Figure 2.2.1).
Also during infections with C. fulvum, transcript levels of RCR3 is up-regulated
(Kruger et al., 2002). Other studies showed that PIP1 is up-regulated during infection
with Pst and P. infestans (Zhao et al., 2003; Tian et al., 2007). RCR3 is required for
recognition of C. fulvum protein Avr2 (Rooney et al., 2005). Furthermore, PIP1 is
inhibited by cystatin-like Epic2B secreted from P. infestans during infection (Tian et
al., 2007). What is striking was that both BTH induced proteases are inhibited by Avr2
and that both are under diversifying selection (Shabab et al., 2008). All variant residues
found in PIP1 and RCR3 are at the surface, around the substrate-binding groove,
possibly affecting the affinity with inhibitors (Figure2.2.2, Shabab et al., 2008).
Diversifying selection at the protein-protein interaction surface often occurs in
plant-pathogen interactions (Reviewed in Misas-Villamil and Van der Hoorn, 2008).
This indicates that BTH-induced proteases are under strong selection pressure caused
by pathogen-derived inhibitors. Indeed, a naturally occurring variant amino acid in
RCR3 prevents the inhibition by Avr2 (Shabab et al., 2008). Taken together these data
26
Discussion
demonstrates that biological functions of PLCPs go beyond the degradation of proteins
under drought or senescence conditions, as they also seem to act in defence.
3.2
PLCPs in abiotic and biotic stress responses
Previous studies have revealed a number of PLCPs with defence-related roles,
including Papain, NbCatB, Mir1 and RD19 (Konno et al., 2004, Gilroy et al., 2007,
Pechan et al., 2002, Bernoux et al., 2008). Our data, with increased Botrytis
susceptibility of Arabidopsis rd21 mutants, supports us to add RD21A as a new
defence-related PLCP (Figure 2.1.2G, 2.1.3F,G). How RD21 is involved in defence to
Botrytis remains to be determined. One possible interpretation is that RD21 is
responsible to restrict cell death. The necrosis induced by Botrytis might be restricted
in the presence of RD21. However, other necrotrophic pathogens, including A.
brassicicola and C. higginsianum, did not show altered susceptibility on rd21 mutant
plants, suggesting that defence the role of RD21 can be a minor for other necrotrophic
pathogens. No changes of transcript levels of RD21/C14 upon BTH treatment were
detected (Figure2.2.1, Appendix 1C). This indicates that RD21 transcript accumulation
is not mediated via SA signalling pathway. PLCPs, in which involved in defence
independent of SA pathway, have already been reported (Zhao et al., 2003).
Microarray data indicate that transcript levels of RD21 do not change by during
Botrytis infection (Appendix 1C). Here, it is only conclusive that RD21 contribute to
defence against Botrytis infection, independent from pathogen perception of SA
signalling pathway in Arabidopsis.
Other pathogens tested on rd21 mutants did not exhibit any phenotype. This
was unexpected, since the activity of RD21 is induced during infection with avirulent
Pst and is suppressed during infection with virulent Pst of Arabidopsis cell culture.
Further studies on potential protease inhibitors of Pst revealed a Chagasin-like
inhibitor named RIP1 (Kaschani and Van der Hoorn, unpublished). RIP1 inhibits the
activity of Arabidopsis RD21 and tomato C14 in vitro and is predicted to be secreted
by the type II secretion system (Kaschani and Van der Hoorn, unpublished). This
suggests that the absence of a phenotype of the rd21 mutant can be due to the presence
of RD21 inhibitors that abolishes RD21 activity in wild-type plants. Yet it is not clear
if RIP1 inhibition to RD21 occurs in vivo during infection and if the Pst rip1 knock-out
has a reduced bacterial growth on rd21 mutant plants.
3.3
RD21 redundancy
It has been assumed that other PLCPs may take over the role of RD21,
27
Discussion
causing less dramatic phenotypic changes of rd21 knock-out plants for Pst and other
pathogens. We first hypothesised that granulin containing PLCPs (RD21B, RD21C and
RD21D) may act redundantly to RD21A. This assumption was based on the presence
of a granulin domain in RD21B, C and D, a feature that is well conserved across plant
species (Schaffer and Fischer, 1990, Linthorst et al., 1993, Tabaeizadeh et al., 1995,
Drake et al., 1996, Yamada et al., 2001, Avrova et al., 1999, Chen et al., 2006, Kikuchi
et al., 2008). The importance of granulin peptides has been well demonstrated in
animal research (Cadieux et al, 2005, Cruts et al., 2006). Granulins act as growth
hormones that contribute to wound induced defence response (Bateman and Bennett,
1998). We were unsuccessful at obtaining the rd21C mutant, though this protease that
is rather expressed in roots, making redundancy with RD21 function in leaves less
likely.
A second source of redundant proteases that are functionally redundant to
RD21 might be the closely related non-granulated versions of RD21A, for example
RDL1 (Figure 1.2). Similarly, RDL2 (At3g19400) might act redundant with RD21C
(At3g19390), since they are highly homologous and probably evolved from an recent
gene duplication. Although many of these proteases were not identified in leaf
proteomes of non infected wild-type Arabidopsis leaves (Van der Hoorn et al., 2004),
these homologues may require particular stress stimuli to trigger activation.
3.4
RD21 and TRV cause cell death
We demonstrated that virus-induced gene silencing of NbRd21 leads to
retarded growth and cell death, independent from Agrobacterium (Figure2.3.3C,
2.3.4B). However, NbRd21 silencing alone is not sufficient to trigger cell death. The
most likely scenario is that the cell death is triggered by the silencing vector, Tobacco
Rattle Virus (TRV). TRV is a well-known plant RNA virus that causes necrosis and
wilting of tobacco, causing leaves rattling in the wind, hence the name. The
introduction of an extra nucleotide sequence in RNA virus suppresses virulence
(Chapman et al., 2008). The same has been observed in case of TRV (Ruiz et al., 1998,
Lu et al., 2003). Our data suggest that NbRd21 silencing enhances TRV symptoms.
This necrosis explains also the retardation of plant growth upon TRV::NbRd21
inoculation.
Cell death caused by TRV and NbRd21 silencing appeared difficult to
uncouple. Although we have detected silencing using hpNbRd21 constructs, this did
not trigger the cell death, even upon additional inoculation with TRV::GFP (Figure
2.3.5A). It has been demonstrated that transient RNAi-based silencing can only silence
28
Discussion
locally and transiently, peaking at 6 dpi (Koscianska et al., 2005, Kalantidis et al.,
2006). The NbRD21 protein might be too stable to disappear using transient RNAi.
This leads to experimental difficulties to synchronise effective silencing and high
production of TRV at the same time.
Himber et al. (2004) found that silencing is stronger at the border of the
silenced region; the formation of ring shaped cell death can be explained by small
RNAs produced in the infiltrated region that can move ten cells, causing a ring of
silencing around the infiltrated area. Presumably, cell death might have been initiated
by TRV at the border of the infiltrated region, where strong silencing occurs. Moreover,
Agrobacterium induces biotic stress that may suppress the cell death (Pruss et al.,
2008). This might explain the formation of a cell death ring. Generation of transgenic
hpNbRd21 N. benthamiana plants is in progress and may help to understand the
mechanism of how cell death occurs upon NbRd21 silencing.
3.5
What is the biochemical function of RD21?
So far, many biochemical characteristics of RD21A have been reported. For
example, activity of RD21 is enhanced by adding of SDS (Yamada et al., 2001, Halls
et al., 2006). However, what the exact biochemical function of RD21 is remains an
open question. We recently found that RD21A can also ligate peptides; in cellular
extracts, RD21 accepts peptides as donor molecules and ligates them, probably through
a thioester intermediate, to unmodified N termini of acceptor proteins, for example
oxygen-evolving complex of photosystem II, PsbP (Wang et al., 2008). This occurs in
extract at neutral to basic pH. It is yet unknown if this also occurs in vivo, since
RD21A presumably resides in acidic compartments. The newly identified function of
RD21A as a potential peptide ligase may helps us to find its client proteins and unravel
the biological role of RD21.
Localization study of RD21A had lead to contrasting data. In case of
Arabidopsis, RD21 is transported directly from the ER bodies into the vacuole
(Hayashi et al., 2001). Tomato C14, one the other hand, localised in nuclei,
chloroplasts and the cytoplasm (Tabaeizadeh et al., 1995). Biochemical assays
revealed that both iRD21 and mRD21 are equally active and acidic pH is required for
the granulin domain release (Hayashi et al., 2001, Van der Hoorn, et al., 2004). This
may suggest that RD21 may act differently in the cells.
There is one report indicating a potential interacting RD21A partners. RD21
from cauliflower caused cleavage of the proform AALP, leading to AALP activation
(Halls et al., 2005). This suggests that RD21 might post-transcriptionally regulate
29
Discussion
AALP. However, we found that when activity-based profiling was applied to rd21A
knock-out lines or NbRd21 silenced plants, active AALP or Alp was detected to the
same level as in control plants, indicating that AALP processing can occur without
RD21 or NbRD21 (Figure 2.1.1, 2.3.1B). Possibly AALP activation by RD21
activation occurs only in vitro. RD21 may also act redundantly with other PLCPs or
the activation is specific for cauliflower.
PDI5 is a protein disulfide isomerase which can oxidize, reduce and isomerise
disulfide bonds, modulate redox responses and chaperone proteins (Ondzighi et al.,
2008). PDI5 is expressed in endothelial cells (seed coat layer) about to undergo PCD in
developing seeds and its mutation results in fewer non viable seeds in Arabidopsis
(Ondzighi et al., 2008). A cytological study demonstrated that PDI5 follows the
trafficking of RD21 from the ER to the vacuole and PDI5 inhibits RD21 in vitro,
implying that RD21 contributes to PCD (Ondzighi et al., 2008). However, rd21 mutants
did not show retarded seeds development and also the inhibition occurs in vivo remains
to be answered.
Other potential RD21-regulating proteins are kunitz-type inhibitors and
cystatins (Halls et al., 2006, Martinez et al., 2005). Sequence analysis shows
kunitz-type inhibitors and all the cystatins carries signal peptides, except cystain1.
Interestingly, drought stress and leaf senescence causes the accumulation of
kunitz-type inhibitors in the cells and specific transcript down-regulation of Cystatin-1
(Halls et al., 2006, Zimmermann et al., 2004). Kunitz-type inhibitors inhibit RD21
activity in vitro under acidic conditions and localises in the vacuole where AALP and
RD21 accumulate (Halls et al., 2006). There are seven cystatins found in Arabidopsis
(Martinez et al., 2005) and some are already described with their biological functions
(Beatrice et al., 2003). Similarly, cystain-5 and cystatin-6 inhibitions and selective
cystain-1 inhibition to RD21A has been revealed using DCG-04 (Both and Van der
Hoorn, unpublished data). Previously a soybean cystatin has been implicated in PCD
regulation (Solomon, et al., 1999). Therefore, it is well possible that these inhibitors
post-translationally regulate the activity of RD21.
3.6
Autophagy and RD21
Autophagy is a dynamic process that involves many proteins with diverse and
unique functions (Bassham, 2007, Table 1.1). Of the seven autophagy-related genes
silenced, we observed that phenotypes upon silencing of ATG3 or ATG6 (beclin)
resembles the phenotype of NbRd21 silencing. ATG3 is an E2-like ligase that can ligate
the ubiquitin-like ATG8 protein to phosphatidylethanolamine (Yamada et al., 2007).
30
Discussion
ATG6/beclin is responsible for activating autophagosome formation together with the
kinase complexes (Thompson and Vierstra, 2005). Although disruption of autophagy
often results in an accelerated senescence phenotype (Hanaoka et al., 2002, Bassham,
2007), abolishment of autophagy function can also cause unlimited PCD (Liu et al.,
2005). We did not observe an accelerated senescence phenotypes neither upon ATG3
nor upon NbRd21 silencing. Comparison of NbRd21 with ATG3 and ATG6 silencing
phenotypes suggests that the role of NbRD21 in autophagy is more related to ATG3
than to ATG6. In fact, unlimited spreading of PCD induced by TMV in ATG6 silenced
N-transgenic plants could not be observed in NbRd21 silenced plants (data not shown,
Liu et al., 2005). This suggests that NbRD21 function is more related to the ATG8
modification than to autophagosome formation, a possible role for RD21 might be
ATG8 processing. For example, ATG4 is a cysteine protease that is required for
C-terminal processing of ATG8 before the ATG3-mediated ligation (Ketelaar et al.,
2004). But yet it is not clear if the ATG8 is cleaved directly by ATG4 or indirectly by
another protease activated by ATG4 (Tanida et al., 2006). Arabidopsis atg4 mutants
display increased chlorosis, accelerated bolting, enhanced dark-induced senescence of
detached leaves and reduced seed yield (Yoshimoto et al., 2004). Phenotypes of
ATG4-silenced N. benthamiana has not been reported. However, since ATG4
modification to ATG8 occurs before the ATG3 ligation step, abolishment of ATG4
function may result in the same phenotype as ATG3 silenced plants. The similar
phenotypes upon ATG3 and NbRd21 silencing suggest NbRd21 is maybe responsible
for ATG4-like ATG8 modification. This can be tested by ATG4 silencing and
investigating ATG8 accumulation in NbRD21 silenced plants. Silencing of ATG8E did
not exhibit the cell death phenotype (Figure 3.3.7A). This is probably due to the
presence of many ATG8 homologues in plants (Bassham et al., 2006).
The presence of cysteine protease inhibitors can affect, autophagy in vivo has been
known for decades (Moriyasu and Ohsumi, 1996). In mammalian studies, adding
cysteine protease inhibitor leupeptin to cells causes the accumulation of autolysosomes
(Kominami et al., 1983). Similarly, plant cells treated with E-64 accumulate particles
of cytoplasm in membrane bound structures, presumably representing plant
autolysosomes (Moriyasu and Ohsumi, 1996). During the final stage of autophagy,
autophagic bodies are degraded in the vacuole and also this process is attenuated by
E-64 (Thompson and Vierstra, 2005). However, which inhibited cysteine proteases are
responsible for these phenotypes has not been determined. Both in vitro and in vivo
DCG-04 labelling showed that RD21 is one of the most prominent proteases in leaves
(Figure2.1.1, Van der Hoorn, et al., 2004). This suggests that the disturbance of
31
Discussion
autophagy by E-64 treatment can be caused by inhibition of RD21. This is supported
by our data showing that ATG3 and ATG6 silencing resulted in an up-regulation of
NbRd21 transcripts without an increased NbRD21 activity. One explanation is that the
transcript levels of NbRd21 is increased upon ATG3 and ATG6 silencing to compensate
for the loss of autophagy, but that RD21 cannot accumulate since the autophagy is
disturbed. The exact role of RD21 in autophagy will need to be further investigated.
3.7
Perspectives
The findings presented in this study allowed us to understand the some of
functional aspects of PLCPs in general and RD21. Yet there are many open questions
left. We found that some of tomato PLCPs are involved in SA signalling pathway,
however it is not yet clear which PLCPs respond to what abiotic or biotic stimuli for
what biological relevance. As we observed, PLCPs, of which are under strong
diversifying selection, seemed to play a role in direct recognition of pathogen derived
inhibitors. The potential inhibitors secreted by pathogens and the diversifying PLCPs
need to be further investigated.
rd21 mutants are more susceptible for Botrytis infection. One can assume that if
RD21 is responsible for restricting the necrosis spread, the question would be why not
other necrotrophic pathogen tested did not display the susceptible phenotype. RNAi
RD21C and other PLCPs knock-out line crossed with rd21ABD mutant can be tested,
if this was due to the redundancy of RD21.
TRV::NbRd21 silencing resulted cell death, probably caused by TRV. Uncoupling
of NbRd21 silencing from TRV is so far unsuccessful. Generation of transgenic
hpNbRd21 N. benthamiana plants is in progress. This may help us to identify the actual
inducer of cell death and to test if the cell death elicitor is replaceable.
Further investigation of the biochemical characteristics of RD21 is required to
understand the function of RD21. Analysis of mutated recombinant RD21 is in
progress. To understand the RD21 regulation mechanisms, in vivo interaction of RD21
previously described in vitro inhibitors are going to be tested.
Atg3 silenced plants pheno-copied NbRd21 silencing. This speculates that NbRd21
contributes to autophagy. Atg4 silenced plants can be generated to test, if NbRD21 is
involved in ATG8 modifications. Co-localization experiment of NbRD21 and ATG8 is
in progress. E-64 caused auto-lysosome accumulation can be tested in NbRd21
silenced plants, to investigate how NbRD21 contribute to autophagy.
32
Materials and Methods
4.
Materials & Methods
4.1. Materials
Chemicals and antibiotics
All chemicals and antibiotics were supplied by Sigma (Deisenhofen, Germany), Roth
(Karlsruhe, Germany), Merck (Darmstadt, Germany) and Duchefa (Haarlem, Germany).
DCG-04 was provided by Dr. Herman Overkleeft (Leiden University, Netherlands) and
Dr. Matt Bogyo (Stanford Medical School, USA) and were synthesized as described
previously (Greenbaum et al., 2002).
Enzymes
Restriction enzymes were from Fermentas (St.Leon-Rot, Germany) and New England
Biolabs (Frankfurt/Main, Germany). Taq polymerase for standard PCR was either from
Promega (Mannheim, Germany) or BioBudget (Krefeld, Germany) and high-fidelity
polymerase was from Roche (Karlsruhe, Germany). Reverse-transcriptase was from
Invitrogen (Karlsruhe, Germany). Ligases were either from Promega (Mannheim,
Germany) or Fermentas (St.Leon-Rot, Germany). DNase and RNase were from Roth
(Karlsruhe, Germany).
Vectors
Plasmids pBlueScriptII KS+ (pBS) and pGEM-T were supplied by Stratagene
(Waldbronn, Germany) and Promega, respectively (Mannheim, Germany). pTRV1 and
pTRV2 vectors were obtained from Dinesh-Kumar (Liu et al., 2002, Lu et al., 2003).
pFK26 CaMV 35S’ promoter containing vector and binary vector pTP05 were described
previously (Shabab et al., 2008).
Kits and primers
Oligonucleotide primers were synthesized by Invitrogen (Karlsruhe, Germany). HPLC
purified primers were generated by Sigma (Deisenhofen, Germany). Oligo(dT) primers
were from Invitrogen (Karlsruhe, Germany) or Roche (Karlsruhe, Germany). Kits for
isolating DNA or RNA were supplied from Qiagen (Hilden, Germany). Plasmid
isolation was carried out using kits of Peqlab (Erlangen, Germany) or Macherey-Nagel
(Duren, Germany).
All primers are listed in Table 4.1 at the end of the Material and Methods section.
33
Materials and Methods
Pathogens
Pseudomonas syringea pv. tomato strain DC3000 (Pst) was obtained from Dr. Silke
Robatzek and Dr. Jane Parker at the MPIZ (Cologne, Germany). Pseudomonas syringea
pv. tomato DC3000 carrying AvrRpm1, AvrRpt2 or AvrRps4 were all obtained from Dr.
Jane Parker. Colletotrichum higginsianum and Hyaloperonospora parasitica isolates
were maintained by members of the Dr. Richard O'Connell and Dr. Jane Parker groups,
respectively. Botrytis cinerea and Alternaria brassicicola were obtained from Dr. Bart
Thomma (Wageningen University, Netherlands).
Bacterial strains
Escherichia coli strain DH10B was used for standard cloning. Agrobacterium
tumefaciens strain GV3101 was used for Agrobacterium-infiltration and plant
transformation.
Plant material
All the Arabidopsis thaliana work was carried out using ecotype Columbia (Col-0),
unless otherwise stated. All the transgenic T-DNA insertion mutants were provided
either by the Salk Institute (http://signal.salk.edu/) or by GABI (http://www.gabi.de/)
and obtained through NASC (http://arabidopsis.info/), except SAIL_781H05 (rd21B)
which was kindly provided by Dr. Czaba Koncz (MPIZ, Cologne, Germany). Genotypes
were all confirmed by PCR on genomic DNA using gene specific primers (Table.4.1).
RD21C screening was performed as described in Rio et al., (2002). Arabidopsis
Landsberg cell suspension culture was obtained from Sainsbury lab (John Innes centre,
Norwich, UK) and maintained according to the method described by Kaffarnik et al.
(2009). N. benthamiana (310A) and tomato (Solanum lycopersicum cv. Money-Maker)
used in this work were grown at the MPIZ (Cologne, Germany). Accession numbers for
tomato relatives, provided by Dr. Klaus Theres are listed below: LA0927 (S.
cheesmaniae), LA1407 (S.cheesmaniae), LA0442 (S. pimpinellifolium); LA1930 (S.
chilense); LA0716 (S. pennellii); LA1777 (S. habrochates/hirsutum); (S. peruvianum);
LA1028 (S. schiewlskii); LA1322 (S. parviflorum); and LA1204 (S. lycopersicum var
cerasiforme).
4.2. Methods
Plant growth conditions
Arabidopsis plants used in this work were either grown in long day (16:8 day/night
34
Materials and Methods
regime) or short day condition (12:12 day/night regime). In case of plants subjected to
pathogen challenges, a short day (day, 24°C; night, 20°C) growth cabinet was used.
Four to five-week old plants were used for experiments, unless otherwise stated.
N. benthamiana and tomato were grown in a climate chamber at a 14-h light regime at
18°C (night) and 22°C (day). Four- to six-week old plants were used for experiments.
BTH treatment was done by watering 5-week-old tomato plants with 25 mg/ml BTH
(Actigard; Syngenta) or water every second day. Samples were taken at 5 days after
starting the BTH treatment, unless otherwise indicated.
Plant transformation
Plants were transformed according to the flower dip method described in Clough and
Bent (1998) with minor changes. A week before the transformation the primary bolts of
plants were clipped and a day before transformation plants were watered and packed in
a plastic bag to create high humidity. 500 ml of overnight grown Agrobacterium culture,
supplemented with 30 mg/l of rifampicin and kanamycin, was centrifuged and the
bacterial pellet resuspended in medium containing 2.3 g/l MS medium and 5% sucrose
at an OD600 of 1. After adding 0.03% Silwet L-77, flower buds were soaked into the
inoculums for ten seconds and plants were covered with a plastic bag overnight, placed
horizontally.
Selection of transformants
Successful transformants were selected on MS media (1.5% agar, 0.05% MES, 1%
sucrose and 0.44% MS salt, pH 5.6) supplemented with 100mg/l kanamycin. Seed
surface sterilization was performed according to the vapour-phase method that produces
chlorine gas by adding hydrochloric acid into commercial bleach in 1:10 dilution
(described at http://plantpath.wisc.edu/~afb/vapster.htm). Two to three-week old plants
showing kanamycin resistance were transferred to soil and T-DNA presence was
confirmed by PCR using insert specific primers (Table. 4.1).
Genomic DNA preparation
Genomic DNA was isolated from plants using method described previously (Thorlby et
al., 2004). Leaf materials were ground in 400 µl Edward buffer (200 mM Tris pH 7.5,
250 mM NaCl, 25 mM EDTA, 0.5% SDS). After centrifugation, the supernatant was
transferred to a new tube and mixed with an equal volume of isopropanol (normally 300
µl). The DNA pellet was precipitated by five minutes centrifugation and dried after
removing the supernatant. DNA was dissolved in 100 µl of H2O without vortexing.
35
Materials and Methods
Crosses
Every flower organs of the acceptor except the carpel was removed from flower buds
using fine forceps. Mature flowers of the donor were selected and used to pollinate the
acceptor carpel. The pollinated acceptor was wrapped with clean film until the seeds
were ready to harvest.
Pathogen assays
Pseudomonas syringea pv. tomato growth assay
Pst DC3000 (with and without Avr genes) was inoculated by spraying as described
previously (Katagiri et al. 2002). The optical density of bacteria in the spray inoculums
was OD600 0.01 to 0.05. Bacterial counts were performed according to the method
described previously (Tornero and Dangl, 2001). Photographs were taken at 4 dpi.
Botrytis cinerea and Alternaria brassicicola pathogen assays
Droplet inoculation of spores was performed as described previously (Thomma et al.,
1998). 5 µl of spore suspension (105 spores/ml) was inoculated on each mature leaves of
4-week old plants. Percentage of fungal infection (fungal out-growth) were scored and
photographed at 5dpi.
Colletotrichum higginsianum pathogen assay
A Colletotrichum higginsianum spore suspension was diluted to 103 spore/ml and 5 µl
droplets were inoculated on leaves of 5-week old plants. Percentage of fungal infection
(fungal out-growth) were scored at 5 dpi. To perform spray inoculation, the spore
suspension was diluted to 104 spore/ml and sprayed onto 3-week old plants. Pictures
were taken at 7 dpi.
Hyaloperonospora parasitica growth assay
Spray inoculation of Hyaloperonospora parasitica was performed according to the
method described previously (Parker at al., 1993). The number of spores were counted
using haemocytometer and were calculated by the formula: (number of spores x dilution
factor)/(counted area x chamber depth).
RNA isolation, cDNA synthesis and analysis and (quantitative) RT-PCR
Total RNA was isolated from tissues frozen in liquid nitrogen using the RNeasy Plant
mini kit (QIAGEN) according to the manufacturer’s guidelines. DNase treatment was
done before the RNA concentration was measured. cDNA was synthesised using
36
Materials and Methods
Superscript II reverse transcriptase and Oligo dT primers. Gene-specific primers are
summarized in Table 4.1. Variant nucleotide analysis was performed as described in
Shabab et al. (2008). Structural models of PIP1 and RCR3 were created as described
previously (Shabab et al., 2008).
For real-time RT-PCR, gene-specific primers were designed using Pearl Primer software
(Table 4.1) (Marshall, 2004). Reaction mixtures for SYBR green (Roche) real-time
RT-PCR were made as described previously (Karsai et al., 2002). DNA synthesis was
recorded with the IQ5 Multicolour Real Time PCR detection system (BioRad).
Threshold cycles were recorded in triplicate over five independent biological samples,
corrected for the Ct of ubiquitin (Rotenberg et al., 2006) and subjected to statistical
analysis following the guidelines of the manufacturer (BioRad).
Cloning for VIGS
Arabidopsis RD21A granulin domain amino acid sequence was used for tBLASTn
search of the TIGR N. benthamiana cDNA database (http://plantta.jcvi.org/) to find two
RD21A-like granulin containing genes in N. benthamiana: TC7740 (NbRd21-I) and
EST748747 (NbRd21-II). NbAlp (TC7311) was found by the same procedure using
Arabidopsis AALP protein sequence as template. Several 300 bp regions were selected
from the cDNA templates and primers were designed carrying restriction sites BamHI
(5’ end) and EcoRI (3’ end) (Table 4.1). N. benthamiana leaf cDNA was used to amplify
the fragments. Cloning vector pBlueScript II KS+ (pBS-II) was digested with restriction
enzymes EcoRI and BamHI and treated with alkaline phosphatase. PCR products were
digested and ligated into pBS-II and the plasmids were transformed into E. coli.
Successful clones, validated by nucleotide sequencing, were digested using the same
restriction enzymes for shuttling into the pTRV2 binary vector (Liu et al. 2002). Inserts
in the pTRV2 plasmid were confirmed by PCR using vector specific primers.
Fragments of autophagy-related genes were cloned into pTRV2 through the procedure as
described above. The template selection was carried out using Arabidopsis cDNA
sequences of ATG7 (AT5G45900), ATG6 (AT3G51840), ATG3 (AT5G61500), ATG5
(AT5G17290) and ATG8E (At2g45170) to find N. benthamiana cDNA sequences of
AY701319, AY701316, AY701318, EB440576 (N. tabacum) and EH369475,
respectively. NcoI-BamHI restriction sites were used to clone all the fragments into the
pTS49 cloning vector (pBluescriptII containing HindIII::35S::NcoI-SalI-BamHI-XhoI
between HindIII-XhoI sites). Primer sequences are listed in Table 4.1). All the fragments
were shuttled into pTRV2 using EcoRI-BamHI sites.
37
Materials and Methods
Agrobacterium infiltration of virus-induced gene silencing construct
pTRV2 plasmids were transformed into Agrobacterium tumefaciens strain GV3101.
Infiltration of Agrobacterium was performed as described previously (Shabab et al.,
2008). Overnight grown Agrobacterium cultures carrying pTRV1 or pTRV2 were
centrifuged and bacteria were resuspended in infiltration buffer (10 mM MES pH 5, 10
mM MgCl2, 1 mM acetosyringone). Cultures were incubated for two to four hours at
room temperature. OD600 was adjusted to 2 and pTRV2-containing cultures were mixed
with pTRV1-containing cultures. Cultures were infiltrated into two leaves of 4-week old
young N. benthamiana plants. Inoculated plants were used at three to six weeks after
infiltration. TRV::GFP (provided by M. Joosten) was used as negative control and by
the bleaching phenotype of TRV::PDS (provided by M. Joosten) was used as a positive
control for silencing.
Co-infiltration of GFP and TRV vectors
For making binary 35S::GFP constructs, template GFP was obtained from the
Panstruga group (MPIZ, Germany). The GFP-encoding fragment was cloned into
pFK26 using primers, GFP-F and GFP-R (See Table 4.1 for sequences), using XhoI-PstI
restriction sites and shuttled into binary vector pTP5 using HindIII-EcoRI sites (Shabab
et al., 2008). After transformation of Agrobacterium, cultures were prepared as
described above and mixed with cultures carrying pTRV1 and pTRV2 in a 1:1 ratio.
Images were generated using the fluorescence microscope.
Trypan blue staining
Trypan blue staining was performed as described previously (Parker et al., 1993).
Whole N. benthamiana leaves were boiled in Trypan blue solution (30 ml lactophenol,
10 mg trypan blue, 30 ml ethanol), destained with chloral hydarate solution (2.5 g/ml
chloral hydrate in H2O) for more than two days and photographed.
Generation of “hairpin” constructs
The same regions of nucleotide sequence as the pTRV2 constructs were chosen to
construct hairpin (hp)NbRD21-I, hpNbRD21-II, hpNbAlp and hpNbCatB. All the
primers used in this work are listed in Table 4.1. A PCR fragment, containing BamHI
site at 3’ and XhoI site at 5’ ends, of Arabidopsis A5tg15070 (part of first intron) was
cloned into a pGEM-T vector to construct pFK29. To clone sense-fragment, PCR
fragments of each gene were cloned into pFK26 using NcoI-BamHI, resulting in pTSX1.
In case of antisense construct, PstI::XhoI-XbaI sites were introduced by PCR and PCR
38
Materials and Methods
products were cloned into pFK29 using PstI-XbaI to make pTSX2. Donor vector pTSX2
was then digested with BamHI and PstI and combined with acceptor vector pTSX1 to
form pTShp. The insert of pTShp was shuttled into binary vector pTP5. Infiltration was
performed as described previously (Shabab et al., 2008).
Infiltration of virons
Leaf disks (1 cm2) of pTRV inoculated plants (4 weeks after infiltration) were ground in
2 ml H2O and centrifuged at 5000 rpm. 1 ml of supernatant was infiltrated into leaves of
6-week old fresh N. benthamiana plants. Pictures were taken at 5 dpi and leaves were
stained with Trypan blue as described above.
Western blot and Activity-based protein profiling
Activity-based protein profiling was performed as described previously with minor
changes (Van der Hoorn et al., 2004). Protein extraction was performed in H2O
containing 10 µM DTT and the extract was centrifuged. 450 µl of supernatant was
mixed with 50 µl 10x buffer (250 mM NaAc (pH 6), 10 µM DTT or 100 mM fresh
L-cysteine) and 1 µl of DCG-04 (1 mg/ml in DMSO). For the negative control, 3 µl of 1
mM E-64 was added for compete DCG-04 labelling. After four to five hours incubation,
1 ml cold acetone was added, vortexed and centrifuged. Supernatant was then discarded
and pellet was washed with 500 µl 70% cold acetone. Pellets were dried at room
temperature and resuspended in 50 µl SDS loading buffer. Samples were loaded onto
polyacrylamide gel (either 12 or 15%) and proteins were transferred to PVDF
membranes. For detecting biotinylated proteins the membrane was incubated with
Ultrasensitive streptavidin-HRP (Sigma, dilution of 1:3000) and signals were detected
using SuperSignal Femto/Pico substrate (Thermo Fisher Scientific, Bonn, Germany) on
X-ray films (Kodak, Germany).
39
Materials and Methods
Table 4.1 Primers
Name
Primer sequence (5'-3')
GABI_401H08f
AGACCTCCGTTACAACCTTCG
GABI_401H08r
CTCCTACGACGAGAAACATGG
GABI_792G08f
CTGAAGAAGAAATGGGGTTCC
GABI_792G08r
CAACAACATCAGCTTACAACAAAAC
SAIL_781H05-f
AATCTACGAAGCGTGGATGG
SAIL_781H05-r
CAGGATTTGAGGGATTTTTCC
SALK_1384831f
CAATGCTGGCTGTAATGGTG
SALK_1384831r
CAGCATTTCCATGAGAAGCA
RD21C1f
GTTAGCGTCGTCAAGAAACTACTCTG
RD21C1r
GACGAGGAAAGTAGTAATACCGAGAG
SALK_10938f
GATCCCATGGCTCTTTCTTCACCTTCAAGAATCC
SALK_10938r
GATCCTGCAGTCACTTAGTTTTGGTGGGGAAAGAAGCC
SALK_124030f
GATCCCATGGCTTTAAAACATATGCAAATCTTTCTC
SALK_124030r
GATCCTGCAGTCATATAGTTGGGTAAGATGCTTTCATGG
SALK_31088f
GATCCCATGGATCGTCTTAAACTTTATTTCTCCG
SALK_31088r
GATCCTGCAGTTAATGGGCGGTGGTTGAGACGGTGGC
SALK_75550f
GATCCCATGGCTGCGAAAACAATCCTATCATCAG
SALK_75550r
GATCCTGCAGTCAAGCCACAACGGGGTATGATGC
SALK_084789f
GAAGCCTCAATAGCCACACTG
SALK_084789r
TATGGCTTTTTCTGCACCATC
SALK_088620f
ATAGGGTTGTCTGCCCAGTTC
SALK_088620r
TAGAACATGACGGGACTGTCC
SALK_019630f
TTGTGTGTGTGTGTTGACTGC
SALK_019630r
AAAACTTACATCACCCCAGCC
SALK_089030f
CGTTGGTCACACATAGTGCAG
SALK_089030r
GACAATACTGGTTGCTCGCAC
SALK_110946f
ACCAAAACCGCAAAGTAATCC
SALK_110946r
TCTAAGACATATGAAGGGGAAATG
SALK_063455f
AACGGTAAAAGCAACCTCGAC
SALK_063455r
TGCCACCGTGAGTTTATTATC
SALK_151526f
AACCAGAAGATCATCTGAAGTGG
SALK_151526r
ATCACTGTCCGACAGGTTCTG
LBa1
TGGTTCACGTAGTGGGCCATCG
LBb1
GCGTGGACCGCTTGCTGCAACT
r112-promf
GGAGAGGACCATTTGGAGAGGACACGT
r113-termr
GATTAGCATGTCACTATGTGTGCATCC
Description
Screening GABI_401H08
Screening GABI_792G08
Screening SAIL_781H05
Screening SALK_1384831
Screening D21C1
Screening SALK_10938
Screening SALK_124030
Screening SALK_31088
Screening SALK_75550
Screening SALK_084789
Screening SALK_088620
Screening SALK_019630
Screening SALK_089030
Screening SALK_110946
Screening SALK_063455
Screening SALK_151526
T-DNA confirmation primer
35's specific primer
40
Materials and Methods
Name
Primer sequence (5'-3')
r114-binf
TAGGTTTACCCGCCAATATATCCTGTC
r115-binr
TTCTGTCAGTTCCAAACGTAAAACGGC
r016-TC1850f1
GATCGGATCCGTTACTGAAAAATGGGAAGCACAC
r017-TC1850r1
GATCGAATTCCCAACCAAATGATCTGAGTTTGAC
r018-TC1850f2
GATCGGATCCTCTGAACAAGTTTGCTGATATGAG
r019-TC1850r2
GATCGAATTCGTCCACCATCACAGCCAGTATTG
r020-TC1850f3
GATCGGATCCCCCTGCTTTTGAGTGGGTGATG
r021-TC1850r3
GATCGAATTCTAGTACTGCATGGGATAAGTC
r028-EST747f7
GATCGGATCCACCCCCTCCACCACCTTCTCCG
r029-EST747r7
GATCGAATTCCTGGCTCTTTAGTGCTTGTACTCC
r030-EST747f8
GATCGGATCCGGTGGACGAAACTCTGAAATGG
r031-EST747r8
GATCGAATTCTTTATTCAAGAATGTACACAGCG
r032-TC9934f9
GATCGGATCCGGCCGGATGGAAAGCTGCACTG
r033-TC9934r9
GATCGAATTCTTGCTGACAGAGAGATATTCAAGCC
r034-TC9934f10
GATCGGATCCCCGATCCACACAGTATCATGAC
r035-TC9934r10
GATCGAATTCGGCTGAAGGCAATCCTGCAACCAC
r036-TC7311f11
GATCGGATCCGAGGTACGAGACAGTTGAGGAG
r037-TC7311r11
GATCGAATTCCCAGCAAGATCCGCACTTGCCCTGG
r038-TC7311f12
GATCGGATCCCATATCCATACACCGGCAAGAATGGC
r039-TC7311r12
GATCGAATTCCCCAATCTGCTCCCCATGAATTCTTC
r040-pTRV2f
GTTACTCAAGGAAGCACGATGAGC
r041-pTRV2r
GTCGAGAATGTCAATCTCGTAGG
NB03-ATG7F2
GATCCCATGGACATTGCCTTCGCTGAATCT
NB04-ATG7R2
GATCGAATTCATGTCCAGGCATCGGAATAG
NB05-ATG6L1
GATCCCATGGCAGTTTGGGAAGGCTATGGA
NB06-ATG6R1
GATCGAATTCTCCCTGTTAACATCTTCAACCTC
NB07-ATG6L2
GATCCCATGGCATCAGGAAGAGAGAGATGCAA
NB08-ATG6R2
GATCGAATTCGAAACTTTGGCCGGAAATG
NB09-ATG3L1
GATCCCATGGAAGGCGTTCTCAGCATCAAT
NB10-ATG3R1
GATCGAATTCGCAAGTTGTCATCCTCGTCA
NB23-ATG5L2
GATCCCATGGCTCCCCCTGCTCTGATTTTA
NB24-ATG5R2
GATCGAATTCACTTTGCACTATCTTCGCCTTC
NB25-ATG8EL
GATCCCATGGGCTGCTCGGATTAGGGAAA
NB26-ATG8ER
GATCGAATTCCCCGAATGTGTTTTCTCCAC
r152-ubif
CGTGAAAACCCTAACGGGGAAGACG
r153-ubir
ATCGCCTCCAGCCTTGTTGTAAACG
r154-actf
ATGAAGCTCAATCCAAGAGGGGTATC
r155-actr
CTCCTGCTCATAGTCAAGAGCCAC
Description
pTP05 specific primer
TRV::NbRd21-Iα cloning
TRV::NbRd21-Iβ cloning
TRV::NbRd21-Iγ cloning
TRV::NbRd21-II cloning
NbRd21-II RT-PCR
TRV::CatB cloning
CatB RT-PCR
TRV::Alp cloning
NbAlp RT-PCR
TRV specific primer
TRV::ATG7 cloning
TRV::ATG6 cloning
TRV::ATG6 cloning
TRV::ATG3 cloning
TRV::ATG5 cloning
TRV::ATG8e cloning
Ubiquitin RT-PCR
NbActin RT-PCR
41
Materials and Methods
Name
Primer sequence (5'-3')
Description
r157-TRVCPf
ATGGGAGATATGTACGATGAATC
r158-TRVCPr
TTCAACTCCATGTTCTCTAACGAAG
r159-NbBeclinf
ATGACGAAAAATAGCAGCAGTAGTAC
r160-NbBeclinr
ACAGTGATGGTGGAGTGAAACCCAG
r161-NbAtg3f
GAAGAGGAGGACATACCTGACATGGGAG
r162-NbAtg3r
CTACCAAGGATCAAAGTCCATGGTG
r163-NbAtg7f
TCCCTGCTTTGGTGCTTGATCCTCG
r164-NbAtg7r
AAGGCTGATGCACCTCGAAACCTTC
GFP-F
ATGCTCGAGGTGAGCAAGGGCGAGGAGC
GFP-R
ATGGGTACCCTGCAGGGATCCTTACTTGTACAGCTCGTCC
T1S1-18x1
GATCCCATGGTCTGAACAAGTTTGCTGATATGAG
T1S2-19x1
GATCGGATCCGTCCACCATCACAGCCAGTATTG
T1S3-18x2
GATCCTCGAGCTGCAGTCTGAACAAGTTTGCTGATATGAG
T1S4-19x2
GATCTCTAGAGTCCACCATCACAGCCAGTATTG
T1S5-20x1
GATCCCATGGCCCTGCTTTTGAGTGGGTGATG
T1S6-21x1
GATCGGATCCTAGTACTGCATGGGATAAGTC
T1S7-20x2
GATCCTCGAGCTGCAGCCCTGCTTTTGAGTGGGTGATG
T1S8-21x2
GATCTCTAGATAGTACTGCATGGGATAAGTC
T2S1-28x1
GATCCCATGGACCCCCTCCACCACCTTCTCCG
T2S2-29x1
GATCGGATCCTAACTTGTATTTGGCTATTCTTC
T2S3-28x2
GATCCTCGAGCTGCAGACCCCCTCCACCACCTTCTCCG
T2S4-29x2
GATCTCTAGATAACTTGTATTTGGCTATTCTTC
T2S5-32x1
GATCCCATGGGGCCGGATGGAAAGCTGCACTG
T2S6-33x1
GATCGGATCCTTGCTGACAGAGAGATATTCAAGCC
T2S7-32x2
GATCCTCGAGCTGCAGGGCCGGATGGAAAGCTGCACTG
T2S8-33x2
GATCTCTAGATTGCTGACAGAGAGATATTCAAGCC
T3S1-36x1
GATCCCATGGGAGGTACGAGACAGTTGAGGAG
T3S2-37x1
GATCGGATCCCCAGCAAGATCCGCACTTGCCCTGG
T3S3-36x2
GATCCTCGAGCTGCAGGAGGTACGAGACAGTTGAGGAG
T3S4-37x2
GATCTCTAGACCAGCAAGATCCGCACTTGCCCTGG
r110f
ATGGCCTCGAGCAGCTCAACTCTCACCATATCC
C14 start, RT-PCR
r057r
AGCTGGATCCTCAAGAACTGCTCTTCTTTCCTCC
C14 stop, RT-PCR
r142f
CTTGGGAACGAAGAGTTCCGGTGACCGG
C14 sequencing
r143f
AAGCTGGTGGCAGAGACTTCCAGCACTAC
r070f
AGCTCCATGGCTTCCAATTTTTTCCTCAAG
PIP1 start, RT-PCR
r071r
CCCCGGATCCTCAAGCAGTAGGGAACGACGCAACC
PIP1 stop, RT-PCR
r144f
TCATTTATGGGGCTCGACACTTCATTAC
PIP1 sequencing
r072f
AGCTCCATGGCTATGAAAGTTGATTTGATG
RCR3 start
TRV specific primers
TRV::ATG6 RT-PCR
TRV::ATG3 RT-PCR
TRV::ATG7 RT-PCR
GFP cloning
hpNbRD21-II pTSX1 cloning
hpNbRD21-II pTSX2 cloning
hpNbRD21-II pTSX1 cloning
hpNbRD21-II pTSX2 cloning
hpNbRD21-II pTSX1 cloning
hpNbRD21-II pTSX2 cloning
hpNbCatB pTSX1 cloning
hpNbCatB pTSX2 cloning
hpNbAlp pTSX1 cloning
hpNbAlp pTSX2 cloning
42
Materials and Methods
Name
Primer sequence (5'-3')
Description
r073r
AGCTCTCGAGCTATGCTATGTTTGGATAAGAAGAC
RCR3 stop
r145f
ACTGGATTAAACATACCTAATTCATATC
RCR3 sequencing
r184f
TGAAGACATTAAATGCAAGCTTCTTACAACAATATTC
RCR3 RT-PCR
r187r
AAGTTCCTCCCGCGTAAAACTGTAAATCTTGGCTAGC
r098f
ATGGCCTCGAGCTCGCTCGTATTGATTCTCGTCG
CYP3 start, RT-PCR
f345r
AAACTGCAGTTAGGCAACGATTGGGTAGGATGC
CYP3 stop, RT-PCR
r146f
GGTATCAATGAGTTTACCGACCTAAC
CYP3 sequencing
r064f
AGCTCTCGAGATGTCACGCTCCTCAGTCCTATTGG
ALP start, RT-PCR
r095r
AGCTCTGCAGTCAGGCAACGACAGGGTAGGATGCACAAG
ALP stop, RT-PCR
r147f
GGGATGAGTTCCGTCGAGTGAAGTTGC
ALP sequencing
r066f
AGCTCCATGGAGCACATAGCCACTTTTTTGC
CatB1 start, RT-PCR
r067r
CCCCTGCAGTTAGTGTTTAGTTGAAGAATTAGC
CatB1 stop, RT-PCR
r148f
GCGCCTTCTTGGAGTTAAGCCCACAAG
CatB1 sequencing
r068f
AGCTCCATGGCCTTGACTTTGAAGTC
CatB2 start, RT-PCR
r069r
AGCTGGATCCCTACATTGAGGCATCAAGGACAGC
CatB2 stop, RT-PCR
r150f
AAGCGCCTTCTTGGAGTTAAGCCTGCA
CatB3 sequencing
r154f
ATGAAGCTCAATCCAAGAGGGGTATC
actin RT-PCR
r155r
CTCCTGCTCATAGTCAAGAGCCAC
r188f
ATAGACGATACTTTAATAAGGACGTTCTCC
r189r
TTGTTACTCACTTGTCTCATGGTATTAGCC
r194f
CAAAACATAAACTGGGATTTAAGAACTGC
r195r
TTTATTATAGTAATGATGATATATGACAC
RT19f
AATATGCTGATCTGACCACTG
RT18r
CCAACAACATCCACATACAC
RT20f
TACAAGCCGTAACTAAACAG
RT21r
TCATATACCCATTCTCACCC
RT01f
CTCATCTTCTCCACCTTATCC
RT02r
GTTCTGTTCGTCTATGTATCTC
RT24f
AAGGACTATCATACAAACTCGG
RT25r
GGCTAACAATACCATCTTTCC
RT05f
GTGTCAATAAGTTTACCGACC
RT06r
CAATACCAGTTTCCCTCCAG
RT11f
TTTCGCTCACTACAAGTCTG
RT12r
ACTCGTTTGTTCCTCTTCTG
RT15f
TTCCTGTTCTAACTCATCCA
RT16r
GGATACAGAAACGATCAGAC
Ubi3f
GCCGACTACAACATCCAGAAGG
Ubi3r
TGCAACACAGCGAGCTTAACC
PR1 RT-PCR
PR4 RT-PCR
PIP1 real time PCR
RCR3 real time PCR
C14 real time PCR
CYP3 real time PCR
ALP real time PCR
CatB1 real time PCR
CatB2 real time PCR
43
ubiquitin real time PCR
Appendix
A
THI1
RDL1
RDL4
ATG6
CEP2
RD19A
CATB1
CEP1
RDL2
PAP5
PAP3
RDL6
ATG9
PAP1
ATG4
ATG4
XCP1
RD21C
CATB2
RD19D
RD21B
RD19C
ATG5
RDL3
ALP2
CATB3
AALP
PAP4
SAG12
RD19B
PAP2
ATG18A
ATG7
RD21A
XCP2
RD21D
ATG3
Appendix 1. Microarray anaysis of 31 PLCPs and autophagy-related genes in Arabidopsis.
B
The cluster analysis of microarray data generated at Geneinvestigator (Zimmermann et al., 2004). Each
column represents a gene. (A) each line represents complied microarray experiments demonstrating the
expression of the gene in different organ of Arabidopsis. (B) each line represents complied microarray
experiments showing the expression of the gene in developmental stages. Blue indicates the gene is
up-regulated.
44
RD21A
XCP2
RD21D
RDL3
ALP2
CATB3
AALP
PAP4
SAG12
RD19B
PAP2
H
XCP1
RD21C
CATB2
RD19D
RD21B
RD19C
THI1
RDL1
RDL4
D
CEP2
RD19A
CATB1
CEP1
RDL2
PAP5
PAP3
RDL6
H
PAP1
C
THI1
RDL1
RDL4
ATG6
CEP2
RD19A
CATB1
CEP1
RDL2
PAP5
PAP3
RDL6
ATG9
PAP1
ATG4
ATG4
XCP1
RD21C
CATB2
RD19D
RD21B
RD19C
ATG5
RDL3
ALP2
CATB3
AALP
PAP4
SAG12
RD19B
PAP2
ATG18A
ATG7
RD21A
XCP2
RD21D
ATG3
Appendix
(C) The cluster analysis of microarray data generated at Geneinvestigator (Zimmermann et al., 2004). Each
column represents a gene. Each line represents complied microarray experiments in which the expression
pattern after given treatment is described left side. Green colour indicates that the gene is down-regulated
and red indicates the gene is up-regulated.
45
C
THI1
RDL1
RDL4
ATG6
CEP2
RD19A
CATB1
CEP1
RDL2
PAP5
PAP3
RDL6
ATG9
PAP1
ATG4
ATG4
XCP1
RD21C
CATB2
RD19D
RD21B
RD19C
ATG5
RDL3
ALP2
CATB3
AALP
PAP4
SAG12
RD19B
PAP2
ATG18A
ATG7
RD21A
XCP2
RD21D
ATG3
Appendix
46
C
THI1
RDL1
RDL4
ATG6
CEP2
RD19A
CATB1
CEP1
RDL2
PAP5
PAP3
RDL6
ATG9
PAP1
ATG4
ATG4
XCP1
RD21C
CATB2
RD19D
RD21B
RD19C
ATG5
RDL3
ALP2
CATB3
AALP
PAP4
SAG12
RD19B
PAP2
ATG18A
ATG7
RD21A
XCP2
RD21D
ATG3
Appendix
47
References
Ahmed, S.U., Rojo, E., Kovaleva, V., Venkataraman, S., Dombrowski, J.E.,
Matsuoka, K., and Raikhel, N.V. (2000) The plant vacuolar sorting receptor
AtELP is involved in transport of NH2-terminal propeptide-containing vacuolar
proteins in Arabidopsis thaliana. Journal of Cell Biology, 149, 1335-1344.
Alvarez, V.E., Kosec, G., Anna, C.S., Turk, V., Cazzulo, J.J., and Turk, B. (2008)
Autophagy is involved in nutritional stress response and differentiation in
Trypanosoma cruzi. Journal of Biological Chemistry, 283, 3454-3464.
Asp, T., Bowra, S., Borg, S., and Holm, P.B. (2004) Molecular cloning, functional
expression in Escherichia coli and enzymatic characterisation of a cysteine
protease from white clover (Trifolium repens). Biochimica Et Biophysica
Acta-Proteins and Proteomics, 1699, 111-122.
Avci, U., Petzold, H.E., Ismail, I.O., Beers, E.P., and Haigler, C.H. (2008) Cysteine
proteases XCP1 and XCP2 aid micro-autolysis within the intact central vacuole
during xylogenesis in Arabidopsis roots. Plant Journal, 56, 303-315.
Avrova, A.O., Stewart, H.E., De Jong, W., Heilbronn, J., Lyon, G.D., and Birch,
P.R.J. (1999) A cysteine protease gene is expressed early in resistant potato
interactions with Phytophthora infestans. Molecular Plant-Microbe Interactions,
12, 1114-1119.
Avrova, A.O., Taleb, N., Rokka, V.M., Heilbronn, J., Campbell, E., Hein, I., Gilroy,
E.M., Cardle, L., Bradshaw, J.E., Stewart, H.E., Fakim, Y.J., Loake, G.,
and Birch, P.R.J. (2004) Potato oxysterol binding protein and cathepsin B are
rapidly up-regulated in independent defence pathways that distinguish R
gene-mediated and field resistances to Phytophthora infestans. Molecular Plant
Pathology, 5, 45-56.
Azarkan, M., Dibiani, R., Baulard, C., and Baeyens-Volant, D. (2006) Effects of
mechanical wounding on Carica papaya cysteine endopeptidases accumulation
and activity. Int J Biol Macromol, 38, 216-224.
Azevedo, C., Betsuyaku, S., Peart, J., Takahashi, A., Noel, L., Sadanandom, A.,
Casais, C., Parker, J., and Shirasu, K. (2006) Role of SGT1 in resistance
protein accumulation in plant immunity. Embo Journal, 25, 2007-2016.
Baker, M., Mackenzie, I.R., Pickering-Brown, S.M., Gass, J., Rademakers, R.,
Lindholm, C., Snowden, J., Adamson, J., Sadovnick, A.D., Rollinson, S.,
Cannon, A., Dwosh, E., Neary, D., Melquist, S., Richardson, A., Dickson, D.,
Berger, Z., Eriksen, J., Robinson, T., Zehr, C., Dickey, C.A., Crook, R.,
McGowan, E., Mann, D., Boeve, B., Feldman, H., and Hutton, M. (2006)
Mutations in progranulin cause tau-negative frontotemporal dementia linked to
chromosome 17. Nature, 442, 916-919.
Bassham, D.C., Laporte, M., Marty, F., Moriyasu, Y., Ohsumi, Y., Olsen, L.J., and
Yoshimoto, K. (2006) Autophagy in development and stress responses of plants.
Autophagy, 2, 2-11.
Bassham, D.C. (2007) Plant autophagy--more than a starvation response. Curr Opin
Plant Biol, 10, 587-593.
Bateman, A., and Bennett, H.P.J. (1998) Granulins: the structure and function of an
emerging family of growth factors. Journal of Endocrinology, 158, 145-151.
Beers, E.P., Jones, A.M., and Dickerman, A.W. (2004) The S8 serine, C1A cysteine
and Al aspartic protease families in Arabidopsis. Phytochemistry, 65, 43-58.
Belenghi, B., Acconcia, F., Trovato, M., Perazzolli, M., Bocedi, A., Polticelli, F.,
48
References
Ascenzi, P., and Delledonne, M. (2003) AtCYS1, a cystatin from Arabidopsis
thaliana, suppresses hypersensitive cell death. European Journal of
Biochemistry, 270, 2593-2604.
Bernoux, M., Timmers, T., Jauneau, A., Briere, C., de Wit, P.J.G.M., Marco, Y.,
and Deslandes, L. (2008) RD19, an Arabidopsis cysteine protease required for
RRS1-R-mediated resistance, is relocalized to the nucleus by the Ralstonia
solanacearum PopP2 effector. Plant Cell, 20, 2252-2264.
Berti, P.J., and Storer, A.C. (1995) Alignment Phylogeny of the Papain Superfamily
of Cysteine Proteases. Journal of Molecular Biology, 246, 273-283.
Beyene, G., Foyer, C.H., and Kunert, K.J. (2006) Two new cysteine proteinases with
specific expression patterns in mature and senescent tobacco (Nicotiana tabacum
L.) leaves. J Exp Bot, 57, 1431-1443.
Brinig, M.M., Register, K.B., Ackermann, M.R., and Relman, D.A. (2006) Genomic
features of Bordetella parapertussis clades with distinct host species specificity.
Genome Biology, 7, -.
Buriankova, K., Doucet-Populaire, F., Dorson, O., Gondran, A., Ghnassia, J.C.,
Weiser, J., and Pernodet, J.L. (2004) Molecular basis of intrinsic macrolide
resistance in the Mycobacterium tuberculosis complex. Antimicrobial Agents
and Chemotherapy, 48, 143-150.
Cadieux, B., Chitramuthu, B.P., Baranowski, D., and Bennett, H.P.J. (2005) The
zebrafish progranulin gene family and antisense transcripts. Bmc Genomics, 6, -.
Carter, C., Pan, S., Zouhar, J., Avila, E.L., Girke, T., and Raikhel, N.V. (2004) The
Vegetative Vacuole Proteome of Arabidopsis thaliana Reveals Predicted and
Unexpected Proteins. The Plant Cell, 16, 3285-3303.
Chang, Y.M., Luthe, D.S., Davis, F.M., and Williams, W.P. (2000) Influence of
whorl region from resistant and susceptible corn genotypes on fall armyworm
(Lepidoptera: Noctuidae) growth and development. J Econ Entomol, 93,
477-483.
Chapman, S., Faulkner, C., Kaiserli, E., Garcia-Mata, C., Savenkov, E.I., Roberts,
A.G., Oparka, K.J., and Christie, J.M. (2008) The photoreversible fluorescent
protein iLOV outperforms GFP as a reporter of plant virus infection. Proc Natl
Acad Sci U S A, 105, 20038-20043.
Chen, R.D., Yu, L.X., Greer, A.F., Cheriti, H., and Tabaeizadeh, Z. (1994) Isolation
of an Osmotic Stress-Induced and Abscisic-Acid-Induced Gene Encoding an
Acidic Endochitinase from Lycopersicon-Chilense. Molecular & General
Genetics, 245, 195-202.
Chen, H.J., Huang, D.J., Hou, W.C., Liu, J.S., and Lin, Y.H. (2006) Molecular
cloning and characterization of a granulin-containing cysteine protease SPCP3
from sweet potato (Ipomoea batatas) senescent leaves. Journal of Plant
Physiology, 163, 863-876.
Clarke, A.K. (2005) Plant proteases - an appetite for destruction. Physiologia
Plantarum, 123, 359-361.
Clough, S.J., and Bent, A.F. (1998) Floral dip: a simplified method for
Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant Journal,
16, 735-743.
Cruts, M., Gijselinck, I., van der Zee, J., Engelborghs, S., Wils, H., Pirici, D.,
Rademakers, R., Vandenberghe, R., Dermaut, B., Martin, J.J., van Duijn,
49
References
C., Peeters, K., Sciot, R., Santens, P., De Pooter, T., Mattheijssens, M., Van
den Broeck, M., Cuijt, I., Vennekens, K., De Deyn, P.P., Kumar-Singh, S.,
and Van Broeckhoven, C. (2006) Null mutations in progranulin cause
ubiquitin-positive frontotemporal dementia linked to chromosome 17q21.
Nature, 442, 920-924.
Drake, R., John, I., Farrell, A., Cooper, W., Schuch, W., and Grierson, D. (1996)
Isolation and analysis of cDNAs encoding tomato cysteine proteases expressed
during leaf senescence. Plant Molecular Biology, 30, 755-767.
Drenth, J., Jansoniu.Jn, Koekoek, R., Swen, H.M., and Wolthers, B.G. (1968)
Structure of Papain. Nature, 218, 929-&.
Eason, J.R., Ryan, D.J., Watson, L.M., Hedderley, D., Christey, M.C., Braun, R.H.,
and Coupe, S.A. (2005) Suppression of the cysteine protease, aleurain, delays
floret senescence in Brassica oleracea. Plant Molecular Biology, 57, 645-657.
El Moussaoui, A., Nijs, M., Paul, C., Wintjens, R., Vincentelli, J., Azarkan, M., and
Looze, Y. (2001) Revisiting the enzymes stored in the laticifers of Carica
papaya in the context of their possible participation in the plant defence
mechanism. Cell Mol Life Sci, 58, 556-570.
Funk, V., Kositsup, B., Zhao, C.S., and Beers, E.P. (2002) The Arabidopsis xylem
peptidase XCP1 is a tracheary element vacuolar protein that may be a papain
ortholog. Plant Physiology, 128, 84-94.
Garcia-Lorenzo, M., Sjodin, A., Jansson, S., and Funk, C. (2006) Protease gene
families in Populus and Arabidopsis. Bmc Plant Biology, 6, -.
Gilroy, E.M., Hein, I., van der Hoorn, R., Boevink, P.C., Venter, E., McLellan, H.,
Kaffarnik, F., Hrubikova, K., Shaw, J., Holeva, M., Lopez, E.C.,
Borras-Hidalgo, O., Pritchard, L., Loake, G.J., Lacomme, C., and Birch,
P.R.J. (2007) Involvement of cathepsin B in the plant disease resistance
hypersensitive response. Plant Journal, 52, 1-13.
Greenbaum, D., Medzihradszky, K.F., Burlingame, A., and Bogyo, M. (2000)
Epoxide electrophiles as activity-dependent cysteine protease profiling and
discovery tools. Chemistry & Biology, 7, 569-581.
Grudkowska, M., and Zagdanska, B. (2004) Multifunctional role of plant cysteine
proteinases. Acta Biochimica Polonica, 51, 609-624.
Guerra, R.R., Kriazhev, L., Hernandez-Blazquez, F.J., and Bateman, A. (2007)
Progranulin is a stress-response factor in fibroblasts subjected to hypoxia and
acidosis. Growth Factors, 25, 280-285.
Halls, C.E., Rogers, S.W., and Rogers, J.C. (2005) Purification of a proaleurain
maturation protease. Plant Science, 168, 1267-1279.
Halls, C.E., Rogers, S.W., Oufattole, M., Ostergard, O., Svensson, B., and Rogers,
J.C. (2006) A Kunitz-type cysteine protease inhibitor from cauliflower and
Arabidopsis. Plant Science, 170, 1102-1110.
Hanaoka, H., Noda, T., Shirano, Y., Kato, T., Hayashi, H., Shibata, D., Tabata, S.,
and Ohsumi, Y. (2002) Leaf senescence and starvation-induced chlorosis are
accelerated by the disruption of an Arabidopsis autophagy gene. Plant Physiol,
129, 1181-1193.
Hanington, P.C., Brennan, L.J., Belosevic, M., and Keddie, B.A. (2008) Molecular
and functional characterization of granulin-like molecules of insects. Insect
Biochemistry and Molecular Biology, 38, 596-603.
50
References
Hao, L., Hsiang, T., and Goodwin, P.H. (2006) Role of two cysteine proteinases in the
susceptible response of Nicotiana benthamiana to Colletotrichum destructivum
and the hypersensitive response to Pseudomonas syringae pv. tomato. Plant
Science, 170, 1001-1009.
Harrak, H., Azelmat, S., Baker, E.N., and Tabaeizadeh, Z. (2001) Isolation and
characterization of a gene encoding a drought-induced cysteine protease in
tomato (Lycopersicon esculentum). Genome, 44, 368-374.
Hayashi, Y., Yamada, K., Shimada, T., Matsushima, R., Nishizawa, N.K.,
Nishimura, M., and Hara-Nishimura, I. (2001) A proteinase-storing body that
prepares for cell death or stresses in the epidermal cells of Arabidopsis. Plant
and Cell Physiology, 42, 894-899.
Himber, C., Dunoyer, P., Moissiard, G., Ritzenthaler, C., and Voinnet, O. (2003)
Transitivity-dependent and -independent cell-to-cell movement of RNA
silencing. Embo J, 22, 4523-4533.
Holwerda, B.C., and Rogers, J.C. (1992) Purification and Characterization of
Aleurain - a Plant Thiol Protease Functionally Homologous to Mammalian
Cathepsin-H. Plant Physiology, 99, 848-855.
Inoue, Y., Suzuki, T., Hattori, M., Yoshimoto, K., Ohsumi, Y., and Moriyasu, Y.
(2006) AtATG genes, homologs of yeast autophagy genes, are involved in
constitutive autophagy in Arabidopsis root tip cells. Plant Cell Physiol, 47,
1641-1652.
Jiang, B., Siregar, U., Willeford, K.O., Luthe, D.S., and Williams, W.P. (1995)
Association of a 33-kilodalton cysteine proteinase found in corn callus with the
inhibition of fall armyworm larval growth. Plant Physiol, 108, 1631-1640.
Jovel, J., Walker, M., and Sanfacon, H. (2007) Recovery of Nicotiana benthamiana
plants from a necrotic response induced by a nepovirus is associated with RNA
silencing but not with reduced virus titer. Journal of Virology, 81, 12285-12297.
Kaffarnik, F.A.R., Jones, A.M.E., Rathjen, J.P., and Peck, S.C. (2009) Effector
Proteins of the Bacterial Pathogen Pseudomonas syringae Alter the Extracellular
Proteome of the Host Plant, Arabidopsis thaliana. Molecular & Cellular
Proteomics, 8, 145-156.
Kalantidis, K., Tsagris, M., and Tabler, M. (2006) Spontaneous short-range silencing
of a GFP transgene in Nicotiana benthamiana is possibly mediated by small
quantities of siRNA that do not trigger systemic silencing. Plant Journal, 45,
1006-1016.
Karsai, A., Muller, S., Platz, S., and Hauser, M.T. (2002) Evaluation of a homemade
SYBR (R) Green I reaction mixture for real-time PCR quantification of gene
expression. Biotechniques, 32, 790-+.
Ketelaar, T., Voss, C., Dimmock, S.A., Thumm, M., and Hussey, P.J. (2004)
Arabidopsis homologues of the autophagy protein Atg8 are a novel family of
microtubule binding proteins. Febs Letters, 567, 302-306.
Kikuchi, Y., Saika, H., Yuasa, K., Nagahama, M., and Tsuji, A. (2008) Isolation and
Biochemical Characterization of Two Forms of RD21 from Cotyledons of
Daikon Radish (Raphanus sativus). Journal of Biochemistry, 144, 789-798.
Koizumi, M., Yamaguchishinozaki, K., Tsuji, H., and Shinozaki, K. (1993)
Structure and Expression of 2 Genes That Encode Distinct Drought-Inducible
Cysteine Proteinases in Arabidopsis-Thaliana. Gene, 129, 175-182.
51
References
Konno, K., Hirayama, C., Nakamura, M., Tateishi, K., Tamura, Y., Hattori, M.,
and Kohno, K. (2004) Papain protects papaya trees from herbivorous insects:
role of cysteine proteases in latex. Plant J, 37, 370-378.
Koscianska, E., Kalantidis, K., Wypijewski, K., Sadowski, J., and Tabler, M.
(2005) Analysis of RNA silencing in agroinfiltrated leaves of Nicotiana
benthamiana and Nicotiana tabacum. Plant Molecular Biology, 59, 647-661.
Kruger, J., Thomas, C.M., Golstein, C., Dixon, M.S., Smoker, M., Tang, S.K.,
Mulder, L., and Jones, J.D.G. (2002) A tomato cysteine protease required for
Cf-2-dependent disease resistance and suppression of autonecrosis. Science, 296,
744-747.
Kruger, J., Thomas, C.M., Golstein, C., Dixon, M.S., Smoker, M., Tang, S., Mulder,
L., and Jones, J.D. (2002) A tomato cysteine protease required for
Cf-2-dependent disease resistance and suppression of autonecrosis. Science, 296,
744-747.
Linthorst, H.J.M., Vanderdoes, C., Vankan, J.A.L., and Bol, J.F. (1993)
Nucleotide-Sequence of a Cdna Clone Encoding Tomato (LycopersiconEsculentum) Cysteine Proteinase. Plant Physiology, 101, 705-706.
Liu, Y.L., Schiff, M., and Dinesh-Kumar, S.P. (2002) Virus-induced gene silencing in
tomato. Plant Journal, 31, 777-786.
Lohman, K.N., Gan, S.S., John, M.C., and Amasino, R.M. (1994) Molecular
Analysis of Natural Leaf Senescence in Arabidopsis-Thaliana. Physiologia
Plantarum, 92, 322-328.
Lu, R., Martin-Hernandez, A.M., Peart, J.R., Malcuit, I., and Baulcombe, D.C.
(2003) Virus-induced gene silencing in plants. Methods, 30, 296-303.
Luderer, R., De Kock, M.J.D., Dees, R.H.L., De Wit, P.J.G.M., and Joosten,
M.H.A.J. (2002) Functional analysis of cysteine residues of ECP elicitor
proteins of the fungal tomato pathogen Cladosporium fulvum. Molecular Plant
Pathology, 3, 91-95.
Marshall, O.J. (2004) PerlPrimer: cross-platform, graphical primer design for standard,
bisulphite and real-time PCR. Bioinformatics, 20, 2471-2472.
Martinez, M., Rubio-Somoza, I., Carbonero, P., and Diaz, I. (2003) A cathepsin
B-like cysteine protease gene from Hordeum vulgare (gene CatB) induced by
GA in aleurone cells is under circadian control in leaves. Journal of
Experimental Botany, 54, 951-959.
Martinez, M., Abraham, Z., Carbonero, P., and Diaz, I. (2005) Comparative
phylogenetic analysis of cystatin gene families from arabidopsis, rice and barley.
Molecular Genetics and Genomics, 273, 423-432.
Moutim, V., Silva, L.G., Lopes, M.T.P., Fernandes, G.W., and Salas, C.E. (1999)
Spontaneous processing of peptides during coagulation of latex from Carica
papaya. Plant Science, 142, 115-121.
Noh, Y.S., and Amasino, R.M. (1999) Identification of a promoter region responsible
for the senescence-specific expression of SAG12. Plant Molecular Biology, 41,
181-194.
Noh, Y.S., and Amasino, R.M. (1999) Regulation of developmental senescence is
conserved between Arabidopsis and Brassica napus. Plant Molecular Biology,
41, 195-206.
Ondzighi, C.A., Christopher, D.A., Cho, E.J., Chang, S.C., and Staehelin, L.A.
52
References
(2008) Arabidopsis protein disulfide isomerase-5 inhibits cysteine proteases
during trafficking to vacuoles before programmed cell death of the endothelium
in developing seeds. Plant Cell, 20, 2205-2220.
Otegui, M.S., Noh, Y.S., Martinez, D.E., Vila Petroff, M.G., Andrew Staehelin, L.,
Amasino, R.M., and Guiamet, J.J. (2005) Senescence-associated vacuoles
with intense proteolytic activity develop in leaves of Arabidopsis and soybean.
Plant Journal, 41, 831-844.
Parker, J.E., Szabo, V., Staskawicz, B.J., Lister, C., Dean, C., Daniels, M.J., and
Jones, J.D.G. (1993) Phenotypic characterization and molecular mapping of the
Arabidopsis-Thaliana locus RPP5, determining disease resistance to
Peronospora-Parasitica. Plant Journal, 4, 821-831.
Peart, J.R., Lu, R., Sadanandom, A., Malcuit, I., Moffett, P., Brice, D.C., Schauser,
L., Jaggard, D.A.W., Xiao, S.Y., Coleman, M.J., Dow, M., Jones, J.D.G.,
Shirasu, K., and Baulcombe, D.C. (2002) Ubiquitin ligase-associated protein
SGT1 is required for host and nonhost disease resistance in plants. Proc Natl
Acad Sci U S A, 99, 10865-10869.
Pechan, T., Jiang, B., Steckler, D., Ye, L., Lin, L., Luthe, D.S., and Williams, W.P.
(1999) Characterization of three distinct cDNA clones encoding cysteine
proteinases from maize (Zea mays L.) callus. Plant Mol Biol, 40, 111-119.
Pechan, T., Ye, L., Chang, Y., Mitra, A., Lin, L., Davis, F.M., Williams, W.P., and
Luthe, D.S. (2000) A unique 33-kD cysteine proteinase accumulates in response
to larval feeding in maize genotypes resistant to fall armyworm and other
Lepidoptera. Plant Cell, 12, 1031-1040.
Pechan, T., Cohen, A., Williams, W.P., and Luthe, D.S. (2002) Insect feeding
mobilizes a unique plant defense protease that disrupts the peritrophic matrix of
caterpillars. Proc Natl Acad Sci U S A, 99, 13319-13323.
Pimpl, P., Hanton, S.L., Taylor, J.P., Pinto-daSilva, L.L., and Denecke, J. (2003)
The GTPase ARF1p controls the sequence-specific vacuolar sorting route to the
lytic vacuole. Plant Cell, 15, 1242-1256.
Rawlings, N.D., Morton, F.R., and Barrett, A.J. (2006) MEROPS: the peptidase
database. Nucleic Acids Research, 34, D270-D272.
Rawlings, N.D., and Morton, F.R. (2008) The MEROPS batch BLAST: A tool to
detect peptidases and their non-peptidase homologues in a genome. Biochimie,
90, 243-259.
Rios, G., Lossow, A., Hertel, B., Breuer, F., Schaefer, S., Broich, M., Kleinow, T.,
Jasik, J., Winter, J., Ferrando, A., Farras, R., Panicot, M., Henriques, R.,
Mariaux, J.B., Oberschall, A., Molnar, G., Berendzen, K., Shukla, V., Lafos,
M., Koncz, Z., Redei, G.P., Schell, J., and Koncz, C. (2002) Rapid
identification of Arabidopsis insertion mutants by non-radioactive detection of
T-DNA tagged genes. Plant Journal, 32, 243-253.
Rooney, H.C., Van't Klooster, J.W., van der Hoorn, R.A., Joosten, M.H., Jones,
J.D., and de Wit, P.J. (2005) Cladosporium Avr2 inhibits tomato Rcr3 protease
required for Cf-2-dependent disease resistance. Science, 308, 1783-1786.
Rotenberg, D., Thompson, T.S., German, T.L., and Willis, D.K. (2006) Methods for
effective real-time RT-PCR analysis of virus-induced gene silencing. Journal of
Virological Methods, 138, 49-59.
Ruiz, M.T., Voinnet, O., and Baulcombe, D.C. (1998) Initiation and maintenance of
53
References
virus-induced gene silencing. Plant Cell, 10, 937-946.
Salas, C.E., Gomes, M.T.R., Hernandez, M., and Lopes, M.T.P. (2008) Plant
cysteine proteinases: Evaluation of the pharmacological activity. Phytochemistry,
69, 2263-2269.
Schaffer, M.A., and Fischer, R.L. (1990) Transcriptional Activation by Heat and Cold
of a Thiol Protease Gene in Tomato. Plant Physiology, 93, 1486-1491.
Seay, M., Patel, S., and Dinesh-Kumar, S.P. (2006) Autophagy and plant innate
immunity. Cell Microbiol, 8, 899-906.
Shabab, M., Shindo, T., Gu, C., Kaschani, F., Pansuriya, T., Chintha, R., Harzen,
A., Colby, T., Kamoun, S., and van der Hoorn, R.A.L. (2008) Fungal effector
protein AVR2 targets diversifying defense-related Cys proteases of tomato.
Plant Cell, 20, 1169-1183.
Shindo, T., and Van Der Hoorn, R.A.L. (2008) Papain-like cysteine proteases: key
players at molecular battlefields employed by both plants and their invaders.
Molecular Plant Pathology, 9, 119-125.
Solomon, M., Belenghi, B., Delledonne, M., Menachem, E., and Levine, A. (1999)
The involvement of cysteine proteases and protease inhibitor genes in the
regulation of programmed cell death in plants. Plant Cell, 11, 431-443.
Svensson, K., Larsson, P., Johansson, D., Bystrom, M., Forsman, M., and
Johansson, A. (2005) Evolution of subspecies of Francisella tularensis. Journal
of Bacteriology, 187, 3903-3908.
Tabaeizadeh, Z., Chamberland, H., Chen, R.D., Yu, L.X., Bellemare, G., and
Lafontaine, J.G. (1995) Identification and immunolocalization of a 65 kda
drought-induced protein in cultivated tomato Lycopersicon-esculentum.
Protoplasma, 186, 208-219.
Taylor, J.A., and West, D.W. (1980) The use of evan blue stain to test the survival of
plant-cells after exposure to high salt and high osmotic-pressure. Journal of
Experimental Botany, 31, 571-576.
Taylor, M.A.J., Baker, K.C., Briggs, G.S., Connerton, I.F., Cummings, N.J., Pratt,
K.A., Revell, D.F., Freedman, R.B., and Goodenough, P.W. (1995)
Recombinant pro-regions from papain and papaya proteinase tv are selective
high-affinity inhibitors of the mature papaya enzymes. Protein Engineering, 8,
59-62.
Thomma, B.P.H.J., Eggermont, K., Penninckx, I.A.M.A., Mauch-Mani, B.,
Vogelsang, R., Cammue, B.P.A., and Broekaert, W.F. (1998) Separate
jasmonate-dependent and salicylate-dependent defense-response pathways in
Arabidopsis are essential for resistance to distinct microbial pathogens. Proc
Natl Acad Sci U S A, 95, 15107-15111.
Thompson, A.R., and Vierstra, R.D. (2005) Autophagic recycling: lessons from yeast
help define the process in plants. Curr Opin Plant Biol, 8, 165-173.
Thorlby, G., Fourrier, N., and Warren, G. (2004) The sensitive to freezing2 gene,
required for freezing tolerance in Arabidopsis thaliana, encodes a
beta-Glucosidase. Plant Cell, 16, 2192-2203.
Tian, M.Y., Win, J., Song, J., van der Hoorn, R., van der Knaap, E., and Kamoun,
S. (2007) A Phytophthora infestans cystatin-like protein targets a novel tomato
papain-like apoplastic protease. Plant Physiology, 143, 364-377.
Tolkatchev, D., Xu, P., and Ni, F. (2001) A peptide derived from the C-terminal part
54
References
of a plant cysteine protease folds into a stack of two beta-hairpins, a scaffold
present in the emerging family of granulin-like growth factors. Journal of
Peptide Research, 57, 227-233.
Tornero, P., and Dangl, J.L. (2001) A high-throughput method for quantifying growth
of phytopathogenic bacteria in Arabidopsis thaliana. Plant Journal, 28, 475-481.
Trobacher, C.P., Senatore, A., and Greenwood, J.S. (2006) Masterminds or minions?
Cysteine proteinases in plant programmed cell death. Canadian Journal of
Botany-Revue Canadienne De Botanique, 84, 651-667.
Tsuji, A., Kikuchi, Y., Ogawa, K., Saika, H., Yuasa, K., and Nagahama, M. (2008)
Purification and characterization of cathepsin B-like cysteine protease from
cotyledons of daikon radish, Raphanus sativus. Febs Journal, 275, 5429-5443.
van der Hoorn, R.A.L., and Jones, J.D. (2004) The plant proteolytic machinery and
its role in defence. Current Opinion in Plant Biology, 7, 400-407.
van der Hoorn, R.A.L., Leeuwenburgh, M.A., Bogyo, M., Joosten, M.H.A.J., and
Peck, S.C. (2004) Activity profiling of papain-like cysteine proteases in plants.
Plant Physiology, 135, 1170-1178.
van der Hoorn, R.A.L. (2008) Plant proteases: From phenotypes to molecular
mechanisms. Annual Review of Plant Biology, 59, 191-223.
Vanderauwera, S., De Block, M., van de Steene, N., de Cottet, B.V., Metzlaff, M.,
and Van Breusegem, F. (2007) Silencing of poly(ADP-ribose) polymerase in
plants alters abiotic stress signal transduction. Proc Natl Acad Sci U S A, 104,
15150-15155.
Vellios, E., Duncan, G., Brown, D., and MacFarlane, S. (2002) Immunogold
localization of tobravirus 2b nematode transmission helper protein associated
with virus particles. Virology, 300, 118-124.
Wang, Z., Gu, C., Colby, T., Shindo, T., Balamurugan, R., Waldmann, H., Kaiser,
M., and van der Hoorn, R.A.L. (2008) beta-Lactone probes identify a
papain-like peptide ligase in Arabidopsis thaliana. Nature Chemical Biology, 4,
557-563.
Wiederanders, B. (2003) Structure-function relationships in class CA1 cysteine
peptidase propeptides. Acta Biochimica Polonica, 50, 691-713.
Yamada, T., Ohta, H., Masuda, T., Ikeda, M., Tomita, N., Ozawa, A., Shioi, Y.,
and Takamiya, K. (1998) Purification of a novel type of SDS-dependent
protease in maize using a monoclonal antibody. Plant and Cell Physiology, 39,
106-114.
Yamada, K., Matsushima, R., Nishimura, M., and Hara-Nishimura, I. (2001) A
slow maturation of a cysteine protease with a granulin domain in the vacuoles of
senescing arabidopsis leaves. Plant Physiology, 127, 1626-1634.
Yamada, T., Kondo, A., Ohta, H., Masuda, T., Shimada, H., and Takamiya, K.
(2001) Isolation of the protease component of maize cysteine protease-cystatin
complex: release of cystatin is not crucial for the activation of the cysteine
protease. Plant Cell Physiol, 42, 710-716.
Yamada, K., Fuji, K., Shimada, T., Nishimura, M., and Hara-Nishimura, I. (2005)
Endosomal proteases facilitate the fusion of endosomes with vacuoles at the
final step of the endocytotic pathway. Plant Journal, 41, 888-898.
Yamada, Y., Suzuki, N.N., Hanada, T., Ichimura, Y., Kumeta, H., Fujioka, Y.,
Ohsumi, Y., and Inagaki, F. (2007) The crystal structure of Atg3, an
55
References
autophagy-related ubiquitin carrier protein (E2) enzyme that mediates Atg8
lipidation. J Biol Chem, 282, 8036-8043.
Yamaguchishinozaki, K., Koizumi, M., Urao, S., and Shinozaki, K. (1992)
Molecular-cloning and characterization of 9 CDNAs for genes that are
responsive to desiccation in Arabidopsis-thaliana - sequence-analysis of one
cdna clone that encodes a putative transmembrane channel protein. Plant and
Cell Physiology, 33, 217-224.
Yoshimoto, K., Hanaoka, H., Sato, S., Kato, T., Tabata, S., Noda, T., and Ohsumi,
Y. (2004) Processing of ATG8s, ubiquitin-like proteins, and their deconjugation
by ATG4s are essential for plant autophagy. Plant Cell, 16, 2967-2983.
Zavasnik-Bergant, T., and Turk, B. (2006) Cysteine cathepsins in the immune
response. Tissue Antigens, 67, 349-355.
Zhao, C.S., Johnson, B.J., Kositsup, B., and Beers, E.P. (2000) Exploiting secondary
growth in Arabidopsis. Construction of xylem and bark cDNA libraries and
cloning of three xylem endopeptidases. Plant Physiology, 123, 1185-1196.
Zhao, Y.F., Thilmony, R., Bender, C.L., Schaller, A., He, S.Y., and Howe, G.A.
(2003) Virulence systems of Pseudomonas syringae pv. tomato promote
bacterial speck disease in tomato by targeting the jasmonate signaling pathway.
Plant Journal, 36, 485-499.
Zimmermann, P., Hirsch-Hoffmann, M., Hennig, L., and Gruissem, W. (2004)
GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox.
Plant Physiology, 136, 2621-2632.
56
Acknowledgments
Acknowledgments
I would like to thank Dr. Renier van der Hoorn for all the support that he provided me throughout my
PhD period at the MPIZ.
Thanks to Professor Reinhard Krämer, Professor Ute Höcker and especially to Professor Paul
Schulze-Lefert for accepting to be the members of my PhD examining committee.
Special thanks to Dr. Gregor Schimiz; for giving his responsibility to act as “Beisitzer” at my exam.
Big thanks to all the members of the van der Hoorn lab, past and present!
Also I have been having good support from the people all around the MPZ! Thanks for everybody!
I would like to thank my friends and former supervisor and colleagues while I was in UK. Without them
most probably I would not be able to start PhD here at MPIZ.
People I met during my stay in Germany in/out of work. It was nice to get to know them and I would like
to thank them too!
I really appreciate the support from my family in Japan throughout my stay in both UK and
Germany. I still feel like the day I arrived in UK was not long ago. But at the same time I feel it was
a long way. After almost ten years of my stay in abroad, here I have finally completed what I aimed
at first!
57
Erklärung
ERKLÄRUNG
Hiermit versichere ich, Takayuki Shindo, dass ich die von mir vorgelegte Dissertation selbständig
angefertigt, die benutzten Quellen und Hilfsmittel vollständig angegeben und die Stellen der Arbeit
-einschließlich Tabellen, Karten und Abbildungen -, die anderen Werken im Wortlaut oder dem Sinn
nach entnommen sind, in jedem Einzelfall als Entlehnung kenntlich gemacht habe; dass diese Dissertation
noch keiner anderen Fakultät oder Universität zur Prüfung vorgelegen hat; dass sie - abgesehen von den
auf Seite I angegebenen Teilpublikationen - noch nicht veröffentlicht worden ist sowie, dass ich eine
solche Veröffentlichung vor Abschluss des Promotionsverfahrens nicht vornehmen werde. Die
Bestimmungen dieser Promotionsordnung sind mir bekannt. Die von mir vorgelegte Dissertation ist von
Prof. Dr. Paul Schulze-Lefert betreut worden.
58
Lebenslauf
LEBENSLAUF
Takayuki SHINDO
______________________________________________________________________
09/99 - 07/00
Qualifekationskurs zum Studium für Ausländer (Foundation course)
Universität von Essex, Essex, UK.
10/00 – 07/04
Bachelors degree in Biologie und Management
Universität von London, Royal Holloway College, Surrey, UK.
09/04 - 09/05
Masters degree in Biologie
Universität von London, Rolyal Holloway Colledge, Surrey, UK.
Abteilung Biologische Wissenschaften
Diplomarbeitsthema: “Identifying the role of the hyper-light sensitive lyn1 mutant in Arabidopsis”
Betreuer: Dr. Enrique Lopez-Juez
SEIT 10/05
Promotionsstudent
Max Planck Institut für Züchtungforschung, Köln, Deutschland
Unabhängige van der Hoorn Arbeitsgruppe
International Max Planck Research School (I.M.P.R.S.)
Dissertationsthema: “Investigating the role of papain-like cysteine protease RD21 in plant-pathogen
interactions”
Betreuer: Dr. Renier A.L. Van der Hoorn
59
60